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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-scitrack">Debian Med / python-scitrack</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc">d6b638cb</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-13T18:10:36+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020.6.5</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#24139dae656713ba861751fb2c2ac38839349a7a">
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.gitattributes
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<li class="file-stats">
<a href="#6b9c6782d59be7c3d669b9e78328b8c384296d32">
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.github/workflows/testing_develop.yml
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.gitignore
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.hgignore
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.hgtags
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LICENSE
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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pyproject.toml
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<a href="#7be999601ee10ece4542da6f9b045dc1b3346ebe">
scitrack/__init__.py
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src/scitrack/__init__.py
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tests/sample-crlf.fasta
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<a href="#05bb45b4ca081053bf18ddd8bfb98ad3b72abf6f">
tests/sample.fasta
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tests/sample-lf.fasta
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<a href="#f996b3e9eb4ba2cf1c9808f7dfe45b052f75a9c6">
tests/test_logging.py
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tox.ini
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<h4>Changes:</h4>
<li id="24139dae656713ba861751fb2c2ac38839349a7a">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#24139dae656713ba861751fb2c2ac38839349a7a"><strong>.gitattributes</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tests/*fasta binary</span></pre>
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<br>
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<li id="6b9c6782d59be7c3d669b9e78328b8c384296d32">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#6b9c6782d59be7c3d669b9e78328b8c384296d32"><strong>.github/workflows/testing_develop.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">CI</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">develop"</span> <span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">develop"</span> <span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">tests</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">${{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">matrix.python-version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">windows-latest</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-latest</span><span class="pi">,</span> <span class="nv" style="color: #008080;">ubuntu-latest</span><span class="pi">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">actions/checkout@v2"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">actions/setup-python@v1"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">${{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">matrix.python-version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">dependencies"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -VV</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m site</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install --upgrade pip setuptools wheel</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install --upgrade tox tox-gh-actions </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Run</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">tox</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">targets</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">for</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">${{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">matrix.python-version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-m</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">tox"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Upload py3.8 coverage to Codecov</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">codecov/codecov-action@v1</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">file</span><span class="pi">:</span> <span class="s" style="color: #d14;">./tests/junit-*.xml</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">fail_ci_if_error</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</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">@@ -26,6 +26,7 @@ pip-log.txt</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">.tox</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">nosetests.xml</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">tests/draw_results</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">*.pytest_cache</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"># Translations</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">*.mo</span>
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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">@@ -21,4 +21,5 @@ dist/*</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">scitrack.egg*</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">*.sublime-*</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">*.wpu</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">*.pytest_cache</span></pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">*.pytest_cache</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">*.tox</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">2c80657fecfe617eab8b5e071da8b4b494ca3636 0.1.6</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">402b7daea661f3904f85f6f248f46c8d9f588704 0.1.7</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">038183f48645c7ba0417fa98946689f86efca803 0.1.8</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">d8aa7076747c991858750c0ecfa5915c6d421d5f 0.1.8.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Copyright 2019-2020 Gavin Huttley</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">|Build Status| |codecov| |Using Black Formatting| |Python 3.6+|</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.. |Build Status| image:: https://github.com/HuttleyLab/scitrack/workflows/CI/badge.svg?branch=develop</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> :target: https://github.com/HuttleyLab/scitrack/actions?workflow=CI</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> :alt: CI Status</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.. |codecov| image:: https://codecov.io/gh/HuttleyLab/scitrack/branch/develop/graph/badge.svg</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> :target: https://codecov.io/gh/HuttleyLab/scitrack</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.. |Using Black Formatting| image:: https://img.shields.io/badge/code%20style-black-000000.svg</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.. |Python 3.6+| image:: https://img.shields.io/badge/python-3.6+-blue.svg</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> :target: https://www.python.org/downloads/release/python-360/</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">About ``scitrack``</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">##################</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">One of the critical challenges in scientific analysis is to track all the elements involved. This includes the arguments provided to a specific application, input data files referenced by those arguments and output data generated by the application. In addition to this, tracking a minimal set of system specific information.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">One of the critical challenges in scientific analysis is to track all the elements involved. This includes the arguments provided to a specific application (including default values), input data files referenced by those arguments and output data generated by the application. In addition to this, tracking a minimal set of system specific information.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">``scitrack`` is a simple package aimed at researchers writing scripts, or more substantial scientific software, to support the tracking of scientific computation. The package provides elementary functionality to support logging. The primary capabilities concern generating checksums on input and output files and facilitating logging of the computational environment.</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">``scitrack`` is a library aimed at application developers writing scientific software to support this tracking of scientific computation. The library provides elementary functionality to support logging. The primary capabilities concern generating checksums on input and output files and facilitating logging of the computational environment</span>.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"><span class="idiff left right">To see some projects using ``scitrack``, see the "Used by" link at the top of the `project GitHub page <https://github.com/HuttleyLab/scitrack>`_</span>.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">**********</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Installing</span>
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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">@@ -30,14 +46,12 @@ And then install::</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">``CachingLogger``</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">*****************</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">There is a single object provided by ``scitrack``, ``CachingLogger``. This object is basically a wrapper around the <span class="idiff left right">``logging`` module, but on invocation,</span> captures basic information regarding the system and the command line call that was made to invoke the application.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">There is a single object provided by ``scitrack``, ``CachingLogger``. This object is basically a wrapper around the <span class="idiff left right">Python standard library ``logging`` module. On invocation, ``CachingLogger``</span> captures basic information regarding the system and the command line call that was made to invoke the application.</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">In addition, the class provides convenience methods for logging both the path and the md5 hexdigest checksum of input/output files. A method is also provided for producing checksums of text data. The latter is useful for the case when data are from a stream or a database, for instance.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">In addition, the class provides convenience methods for logging both the path and the md5 hexdigest checksum <span class="idiff left right">[1]_ </span>of input/output files. A method is also provided for producing checksums of text data. The latter is useful for the case when data are from a stream or a database, for instance.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">All logging calls are cached until a path for a logfile is provided. The logger can also, optionally, create directories.</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">When run in parallel using ``mpirun``, the process ID is appended to the hostname to help identify processors.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">**********************************</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Simple instantiation of the logger</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">**********************************</span>
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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">@@ -49,7 +63,6 @@ Creating the logger. Setting ``create_dir=True`` means on creation of the logfil</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> from scitrack import CachingLogger</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> LOGGER = CachingLogger(create_dir=True)</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> LOGGER.log_file_path = "somedir/some_path.log"</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">The last assignment triggers creation of ``somedir/some_path.log``.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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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">@@ -57,40 +70,38 @@ The last assignment triggers creation of ``somedir/some_path.log``.</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">Capturing a programs arguments and options</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">******************************************</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">``scitrack`` will write the contents of ``sys.argv`` to the log file, prefixed by ``command_string``. However, this only captures arguments specified on the command line. Tracking the value of optional arguments not specified, which may have default values, is critical to tracking the full command set. Doing this is <span class="idiff left right">your responsibility as a developer</span>.</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">``scitrack`` will write the contents of ``sys.argv`` to the log file, prefixed by ``command_string``. However, this only captures arguments specified on the command line. Tracking the value of optional arguments not specified, which may have default values, is critical to tracking the full command set. Doing this is <span class="idiff left right">now easy with the simple statement ``LOGGER.log_args()``. The logger can also record the versions of named dependencies</span>.</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">Here's one approach <span class="idiff left right">when</span> using the ``click`` `command line interface library <http://click.pocoo.org/>`_. Below we create a simple ``click`` app and capture the required and optional argument values.</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">Here's one approach <span class="idiff left right">to incorporating ``scitrack`` into a command line application built</span> using the ``click`` `command line interface library <http://click.pocoo.org/>`_. Below we create a simple ``click`` app and capture the required and optional argument values.</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> from scitrack import CachingLogger</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> import click</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> from scitrack import CachingLogger</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> LOGGER = CachingLogger()</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> @click.group()</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> def main():</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> """the main command"""</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> pass</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> @<span class="idiff left right">main</span>.command()</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> @click.option(<span class="idiff left right">'-i', '--infile'</span>, type=click.Path(exists=True))</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> @click.option(<span class="idiff left right">'-t', '--test', is_flag=True, help='Run test.'</span>)</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> def m<span class="idiff left right">y_app</span>(infile, test):</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> @<span class="idiff left right">click</span>.command()</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> @click.option(<span class="idiff left right">"-i", "--infile"</span>, type=click.Path(exists=True))</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> @click.option(<span class="idiff left right">"-t", "--test", is_flag=True, help="Run test."</span>)</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> def m<span class="idiff left right">ain</span>(infile, test):</span>
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80
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> # capture the local variables, at this point just provided arguments</span>
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81
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> LOGGER.log_args()</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> LOGGER.log_versions(<span class="idiff left right">'numpy'</span>)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> LOGGER.log_versions(<span class="idiff left right">"numpy"</span>)</span>
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83
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> LOGGER.input_file(infile)</span>
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84
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> LOGGER.log_file_path = "some_path.log"</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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86
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> if __name__ == "__main__":</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> m<span class="idiff left right">y_app</span>()</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> m<span class="idiff left right">ain</span>()</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">The ``CachingLogger.write()`` method takes a message and a label. All other logging methods wrap ``log_message()``, providing a specific label. For instance, the method ``input_file()`` writes out two lines in the log.</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">- <span class="idiff left right">input_file_path</span>, the absolute path to the intput file</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">- <span class="idiff left right">input_file_path md5sum</span>, the hex digest of the file</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">- <span class="idiff left right">``input_file_path``</span>, the absolute path to the intput file</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">- <span class="idiff left right">``input_file_path md5sum``</span>, the hex digest of the file</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">``output_file()`` behaves analogously. An additional method ``text_data()`` is useful for other data input/output sources (e.g. records from a database). For this to have value for arbitrary data types requires a systematic approach to ensuring the text conversion is robust across platforms.</span>
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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">@@ -104,17 +115,26 @@ Some sample output</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO system_details : system=Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO python : 3.7.1</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO user : gavin</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO command_string : /Users/gavin/miniconda3/envs/py37/bin/py.test -s</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO input_file_path : /Users/gavin/repos/SciTrack/tests/sample.fasta</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO input_file_path md5sum : 96eb2c2632bae19eb65ea9224aaafdad</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> 2018-11-28 11:33:30 yourmachine.com:71779 INFO version : numpy==1.15.1</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO system_details : system=Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO python : 3.8.2</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO user : gavin</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO command_string : ./demo.py -i /Users/gavin/repos/SciTrack/tests/sample-lf.fasta</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO params : {'infile': '/Users/gavin/repos/SciTrack/tests/sample-lf.fasta', 'test': False}</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO version : __main__==None</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO version : numpy==1.18.4</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO input_file_path : /Users/gavin/repos/SciTrack/tests/sample-lf.fasta</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> 2020-05-25 13:32:07 Eratosthenes:98447 INFO input_file_path md5sum : 96eb2c2632bae19eb65ea9224aaafdad</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext">**********************</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext">Other useful functions</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">**********************</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">Two other useful functions are ``get_file_hexdigest`` and ``get_text_hexdigest``. The latter can take either unicode or ascii strings.</span></pre>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Two other useful functions are ``get_file_hexdigest`` and ``get_text_hexdigest``.</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">****************</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Reporting issues</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">****************</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">Use the project `issue tracker <https://github.com/HuttleyLab/scitrack/issues>`_.</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.. [1] The hexdigest serves as a unique signature of a files contents.</span></pre>
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<li id="5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="toml"><span class="nn" style="color: #555;">[build-system]</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="toml"><span class="py">requires</span> <span class="p">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"setuptools>=40.6.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wheel"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="toml"><span class="py">build-backend</span> <span class="p">=</span> <span class="s" style="color: #d14;">"setuptools.build_meta"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="toml"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.black]</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="toml"><span class="py">line-length</span> <span class="p">=</span> <span class="mi" style="color: #099;">88</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="toml"><span class="py">exclude</span> <span class="p">=</span> <span class="s" style="color: #d14;">'''</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="toml"><span class="s" style="color: #d14;">/(</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="toml"><span class="s" style="color: #d14;"> \.eggs</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="toml"><span class="s" style="color: #d14;"> | \.git</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="toml"><span class="s" style="color: #d14;"> | \.hg</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="toml"><span class="s" style="color: #d14;"> | \.mypy_cache</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="toml"><span class="s" style="color: #d14;"> | \.tox</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="toml"><span class="s" style="color: #d14;"> | \.venv</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="toml"><span class="s" style="color: #d14;"> | _build</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="toml"><span class="s" style="color: #d14;"> | build</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="toml"><span class="s" style="color: #d14;"> | dist</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="toml"><span class="s" style="color: #d14;"> | tests/data</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="toml"><span class="s" style="color: #d14;">)/</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="toml"><span class="s" style="color: #d14;">'''</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="toml"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.isort]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="toml"><span class="py">atomic</span><span class="p">=</span><span class="kc" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="toml"><span class="py">force_grid_wrap</span><span class="p">=</span><span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="toml"><span class="py">include_trailing_comma</span><span class="p">=</span><span class="kc" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num new new_line" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="toml"><span class="py">lines_after_imports</span><span class="p">=</span><span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="toml"><span class="py">lines_between_types</span><span class="p">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="toml"><span class="py">multi_line_output</span><span class="p">=</span><span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="toml"><span class="py">use_parentheses</span><span class="p">=</span><span class="kc" style="font-weight: 600;">true</span></span></pre>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pathlib</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">find_packages</span><span class="p">,</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016, Gavin Huttley"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016<span class="idiff left right">-2020</span>, Gavin Huttley"</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Gavin Huttley"</span><span class="p">]</span></span>
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9
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<td class="diff-line-num new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BSD"</span></span>
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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0.1.8.1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">2020.6.5</span>"</span></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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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12
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<td class="diff-line-num new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin.Huttley@anu.edu.au"</span></span>
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__status__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Development"</span></span>
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14
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">py_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Python-3.6 or greater is required, Python-%s used."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">py_version</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"Python-3.6 or greater is required, Python-%s used."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">py_version</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">PROJECT_URLS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">"Documentation"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"Bug Tracker"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack/issues"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"Source Code"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">short_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"scitrack"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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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">@@ -22,6 +32,8 @@ readme_path = pathlib.Path(__file__).parent / "README.rst"</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readme_path</span><span class="p">.</span><span class="n" style="color: #333;">read_text</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">PACKAGE_DIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"src"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"scitrack"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span></span>
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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">@@ -29,18 +41,23 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gavin.huttley@anu.edu.au"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">short_description</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"text/x-rst"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">platforms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"any"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">__license__</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"science"</span><span class="p">,</span> <span class="s" style="color: #d14;">"logging"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"parallel"</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"science"</span><span class="p">,</span> <span class="s" style="color: #d14;">"logging"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 3 - Alpha"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: BSD License"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Software Development :: Libraries :: Python Modules"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"Operating System :: OS Independent"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"scitrack"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 4 - Beta"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: BSD License"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Software Development :: Libraries :: Python Modules"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">"Operating System :: OS Independent"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.6"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.7"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.8"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(</span><span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"src"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">""</span><span class="p">:</span> <span class="n" style="color: #333;">PACKAGE_DIR</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">project_urls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PROJECT_URLS</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="p">)</span></span></pre>
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<li id="7be999601ee10ece4542da6f9b045dc1b3346ebe">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#7be999601ee10ece4542da6f9b045dc1b3346ebe"><strong>scitrack/__init__.py</strong>
→
<strong>src/scitrack/__init__.py</strong>
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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">@@ -6,13 +6,15 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">socket</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">getpass</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">getuser</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016, Gavin Huttley"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016<span class="idiff left right">-2020</span>, Gavin Huttley"</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Gavin Huttley"</span><span class="p">]</span></span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BSD"</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0.1.8.1</span>"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">2020.6.5</span>"</span></span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin.Huttley@anu.edu.au"</span></span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">__status__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Development"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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">@@ -93,14 +95,16 @@ class CachingLogger(object):</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_file_path</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_reset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">):</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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97
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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98
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_started</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_messages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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101
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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103
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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105
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log_file_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_file_path</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" 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">@@ -196,9 +200,6 @@ class CachingLogger(object):</td>
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196
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">shutdown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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197
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">"""safely shutdown the logger"""</span></span>
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198
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">().</span><span class="n" style="color: #333;">removeHandler</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_logfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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202
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reset</span><span class="p">()</span></span>
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203
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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204
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log_versions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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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">@@ -280,9 +281,12 @@ def get_text_hexdigest(data):</td>
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280
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> This will occur if the line ending character differs from being read in</span></span>
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281
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> 'rb' versus 'r' modes.</span></span>
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282
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">,</span> <span class="s" style="color: #d14;">u""</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">):</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"can only checksum string or unicode data"</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">data_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data_class</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">,</span> <span class="s" style="color: #d14;">u""</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">):</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">b""</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"can only checksum string, unicode or bytes data"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">md5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">md5</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">md5</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span></pre>
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<pre style="margin: 0;">B<span id="LC1" class="line" lang="plaintext">>Rhesus with extra words</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TemporaryDirectory</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scitrack</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">CachingLogger</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">get_file_hexdigest</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">get_package_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">get_version_for_package</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scitrack</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">CachingLogger</span><span class="p">,</span> <span class="n" style="color: #333;">get_package_name</span><span class="p">,</span> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">get_version_for_package</span><span class="p">,</span> <span class="n" style="color: #333;">logging</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016, Gavin Huttley"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2016<span class="idiff left right">-2020</span>, Gavin Huttley"</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Gavin Huttley"</span><span class="p">]</span></span>
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15
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<td class="diff-line-num new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BSD"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0.1.8.1</span>"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">2020.6.5</span>"</span></span>
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17
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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18
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<td class="diff-line-num new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gavin.Huttley@anu.edu.au"</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">__status__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Development"</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">LOGFILE_NAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"delme.log"</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">DIRNAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"delme"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">).</span><span class="n" style="color: #333;">parent</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">DIRNAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"delme"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">LOGFILE_NAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DIRNAME</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"delme.log"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_creates_path</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"""creates a log path"""</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">DIRNAME</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"sample</span>.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_ROOTDIR</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample-lf</span>.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">,</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">DIRNAME</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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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">@@ -39,15 +50,18 @@ def test_creates_path():</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_args</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"""details on host, python version should be present in log"""</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"sample</span>.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_ROOTDIR</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample-lf</span>.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"system_details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">,</span> <span class="s" style="color: #d14;">"user"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command_string"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">.</span><span class="n" style="color: #333;">read_text</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"system_details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">,</span> <span class="s" style="color: #d14;">"user"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command_string"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">f"</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">label</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">LOGFILE_</span>NAME</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shutil</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmtree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DIR</span>NAME</span><span class="p">)</span></span>
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51
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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52
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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53
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" 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="69" 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">@@ -55,7 +69,7 @@ def test_tracks_args():</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_locals</span><span class="p">():</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"""details on local arguments should be present in log"""</span></span>
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57
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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59
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">track_func</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"abc"</span><span class="p">):</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_args</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" 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="83" 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">@@ -69,9 +83,9 @@ def test_tracks_locals():</td>
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69
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"params :"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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70
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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71
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"abc"</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"></span>
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72
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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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">@@ -100,23 +114,78 @@ def test_package_versioning():</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_versions</span><span class="p">():</span></span>
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101
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"""should track versions"""</span></span>
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102
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"sample</span>.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_ROOTDIR</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample-lf</span>.fasta"</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_versions</span><span class="p">([</span><span class="s" style="color: #d14;">"numpy"</span><span class="p">])</span></span>
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106
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">())</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"system_details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">,</span> <span class="s" style="color: #d14;">"user"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command_string"</span><span class="p">]:</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">))</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version :"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"==%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version__</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">contents</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">.</span><span class="n" style="color: #333;">read_text</span><span class="p">()</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"system_details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">,</span> <span class="s" style="color: #d14;">"user"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command_string"</span><span class="p">]:</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">f"</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">label</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">),</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version :"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"==%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version__</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_caching</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"""should cache calls prior to logging"""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"sample-lf.fasta"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">_messages</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"md5sum"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">_messages</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_versions</span><span class="p">([</span><span class="s" style="color: #d14;">"numpy"</span><span class="p">])</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"numpy=="</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">_messages</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_shutdown</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">"""correctly purges contents"""</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_versions_empty</span><span class="p">():</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">"""should track version of scitrack"""</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_versions</span><span class="p">()</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">.</span><span class="n" style="color: #333;">read_text</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"system_details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">,</span> <span class="s" style="color: #d14;">"user"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command_string"</span><span class="p">]:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">f"</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">label</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">),</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version :"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"==%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version__</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"></span>
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118
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<td class="diff-line-num new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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119
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<td class="diff-line-num new_line old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">LOGFILE_</span>NAME</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shutil</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmtree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DIR</span>NAME</span><span class="p">)</span></span>
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120
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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121
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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122
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" 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="193" 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">@@ -124,7 +193,7 @@ def test_tracks_versions():</td>
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124
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_versions_string</span><span class="p">():</span></span>
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125
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">"""should track version if package name is a string"""</span></span>
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126
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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128
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_versions</span><span class="p">(</span><span class="s" style="color: #d14;">"numpy"</span><span class="p">)</span></span>
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129
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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130
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" 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="205" 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">@@ -136,16 +205,42 @@ def test_tracks_versions_string():</td>
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136
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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137
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version :"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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138
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"></span>
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139
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">LOGFILE_</span>NAME</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shutil</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmtree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DIR</span>NAME</span><span class="p">)</span></span>
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141
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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142
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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144
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_version_for_package</span><span class="p">():</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"""should track version if package is a module"""</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_version_for_package</span><span class="p">(</span><span class="n" style="color: #333;">numpy</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># one with a callable</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">pyfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"delme.py"</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">pyfile</span><span class="p">.</span><span class="n" style="color: #333;">write_text</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">"def version():"</span><span class="p">,</span> <span class="s" style="color: #d14;">" return 'my-version'"</span><span class="p">]))</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">delme</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_version_for_package</span><span class="p">(</span><span class="s" style="color: #d14;">"delme"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"my-version"</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">pyfile</span><span class="p">.</span><span class="n" style="color: #333;">unlink</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># func returns a list</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">pyfile</span><span class="p">.</span><span class="n" style="color: #333;">write_text</span><span class="p">(</span><span class="s" style="color: #d14;">"version = ['my-version']</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">importlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">reload</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_version_for_package</span><span class="p">(</span><span class="nb" style="color: #0086b3;">reload</span><span class="p">(</span><span class="n" style="color: #333;">delme</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"my-version"</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">pyfile</span><span class="p">.</span><span class="n" style="color: #333;">unlink</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tracks_versions_module</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">"""should track version if package is a module"""</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">LOGFILE_NAME</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LOGFILE_NAME</span></span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"numpy==%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span></span>
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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">@@ -157,8 +252,9 @@ def test_tracks_versions_module():</td>
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157
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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158
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<td class="diff-line-num new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version :"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"numpy"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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159
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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160
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<td class="diff-line-num new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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161
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<td class="diff-line-num new_line old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">LOGFILE_</span>NAME</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="162" 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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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shutil</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmtree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DIR</span>NAME</span><span class="p">)</span></span>
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162
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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163
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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164
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" 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="263" 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">@@ -167,7 +263,7 @@ def test_appending():</td>
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167
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="s" style="color: #d14;">"""appending to an existing logfile should work"""</span></span>
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<td class="diff-line-num old_line" data-linenumber="168" 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">
168
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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169
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"sample</span>.fasta"</span><span class="p">)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_ROOTDIR</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample-lf</span>.fasta"</span><span class="p">)</span></span>
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171
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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172
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">()</span></span>
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173
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" 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="274" 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">@@ -178,7 +274,7 @@ def test_appending():</td>
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178
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a"</span></span>
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180
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"sample</span>.fasta"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_ROOTDIR</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample-lf</span>.fasta"</span><span class="p">)</span></span>
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182
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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183
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"></span>
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184
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="286" 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">@@ -190,7 +286,7 @@ def test_appending():</td>
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190
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="mi" style="color: #099;">2</span><span class="p">}</span></span>
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191
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"></span>
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192
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">LOGFILE_</span>NAME</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shutil</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmtree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DIR</span>NAME</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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195
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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196
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" 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="294" 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">@@ -198,30 +294,137 @@ def test_appending():</td>
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198
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mdsum_input</span><span class="p">():</span></span>
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199
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="s" style="color: #d14;">"""md5 sum of input file should be correct"""</span></span>
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200
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="s" style="color: #d14;">"sample.fasta"</span><span class="p">)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># first file has LF, second has CRLF line endings</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">hex_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"96eb2c2632bae19eb65ea9224aaafdad"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">),</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"e7e219f66be15d8afc7cdb85303305a7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-crlf.fasta"</span><span class="p">),</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="p">]</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-crlf.fasta"</span><span class="p">)</span></span>
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203
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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204
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"></span>
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205
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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206
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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207
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"input_file_path md5sum"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"96eb2c2632bae19eb65ea9224aaafdad"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hex_path</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"input_file"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hex_path</span><span class="p">)</span></span>
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213
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"></span>
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mdsum_output</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="s" style="color: #d14;">"""md5 sum of output file should be correct"""</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># first file has LF, second has CRLF line endings</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">hex_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"96eb2c2632bae19eb65ea9224aaafdad"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="p">]</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">output_file</span><span class="p">(</span><span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hex_path</span><span class="p">:</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hex_path</span><span class="p">)</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_logging_text</span><span class="p">():</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="s" style="color: #d14;">"""correctly logs text data"""</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"abcde</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">edfgu</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">yhbnd"</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">hexd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"f06597f8a983dfc93744192b505a8af9"</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">text_data</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"UNIQUE"</span><span class="p">)</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">.</span><span class="n" style="color: #333;">read_text</span><span class="p">().</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">unique</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contents</span><span class="p">:</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"UNIQUE"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">unique</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">hexd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unique</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_logfile_path</span><span class="p">():</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">"""correctly assigned"""</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CachingLogger</span><span class="p">(</span><span class="n" style="color: #333;">create_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">log_file_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">log_file_path</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">LOGFILE_NAME</span><span class="p">)</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">LOGGER</span><span class="p">.</span><span class="n" style="color: #333;">shutdown</span><span class="p">()</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">DIRNAME</span><span class="p">)</span></span>
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216
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"></span>
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219
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"></span>
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_md5sum_text</span><span class="p">():</span></span>
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221
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="s" style="color: #d14;">"""md5 sum for text data should be computed"""</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">u</span>"åbcde"</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"åbcde"</span></span>
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223
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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224
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span></span>
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225
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"abcde"</span></span>
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226
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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227
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># loading contents from files with diff line-endings and check</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">hex_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"96eb2c2632bae19eb65ea9224aaafdad"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-lf.fasta"</span><span class="p">),</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"e7e219f66be15d8afc7cdb85303305a7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-crlf.fasta"</span><span class="p">),</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="p">]</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hex_path</span><span class="p">:</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TEST_ROOTDIR</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">p</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">read_bytes</span><span class="p">()</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_text_hexdigest_invalid</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="s" style="color: #d14;">"""raises TypeError when invalid data provided"""</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">([])</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_from_written</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="s" style="color: #d14;">"""create files with different line endings dynamically"""</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"abcdeENDedfguENDyhbnd"</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">TEST_ROOTDIR</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dirname</span><span class="p">:</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ex</span><span class="p">,</span> <span class="n" style="color: #333;">lf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"f06597f8a983dfc93744192b505a8af9"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"39db5cc2f7749f02e0c712a3ece12ffc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r\n</span><span class="s" style="color: #d14;">"</span><span class="p">),</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="p">):</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"test.txt"</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">,</span> <span class="n" style="color: #333;">lf</span><span class="p">)</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">write_bytes</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">))</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_text_hexdigest</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ex</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_file_hexdigest</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">got</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="s" style="color: #d14;">f"FAILED: </span><span class="si" style="color: #d14;">{</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">lf</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">, </span><span class="si" style="color: #d14;">{</span><span class="p">(</span><span class="n" style="color: #333;">ex</span><span class="p">,</span> <span class="n" style="color: #333;">got</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/d6b638cb2bed1131fe63e61a81a0446d40896cfc#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="ini"><span class="nn" style="color: #555;">[tox]</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">py36, py37, py38</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="ini"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv]</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="ini"><span class="py">passenv</span> <span class="p">=</span> <span class="s" style="color: #d14;">*</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span> <span class="s" style="color: #d14;">numpy</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">click</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest-cov</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="ini"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:py38]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="ini"><span class="py">changedir</span> <span class="p">=</span> <span class="s" style="color: #d14;">tests</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.8</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest</span> <span class="py">--junitxml</span><span class="p">=</span><span class="s" style="color: #d14;">junit-{envname}.xml --cov-report xml --cov=scitrack</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="ini"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:py37]</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="ini"><span class="py">changedir</span> <span class="p">=</span> <span class="s" style="color: #d14;">tests</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.7</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest</span> <span class="py">--junitxml</span><span class="p">=</span><span class="s" style="color: #d14;">junit-{envname}.xml --cov-report xml --cov=scitrack</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="ini"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:py36]</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="ini"><span class="py">changedir</span> <span class="p">=</span> <span class="s" style="color: #d14;">tests</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.6</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest</span> <span class="py">--junitxml</span><span class="p">=</span><span class="s" style="color: #d14;">junit-{envname}.xml --cov-report xml --cov=scitrack</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="ini"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="ini"><span class="nn" style="color: #555;">[gh-actions]</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="ini"><span class="py">python</span> <span class="p">=</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3.6:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">py36</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3.7:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">py37</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3.8:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">py38</span></span></pre>
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