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<h3>
Nilesh Patra pushed to branch master
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/33dea32fee15d42a636bbba5b4a3bdc8eb760ea9">33dea32f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:43:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: Fix watch regex
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/ff1dc2ab9e72c3b736b49d402631f813b43e893f">ff1dc2ab</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:44:20+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.5.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/2eace5f3b11ec4fe0dbf2a4f3406aa0e129bf944">2eace5f3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:44:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021.5.3'
Update to upstream version '2021.5.3'
with Debian dir fcee547153b34840afff1acd79b9d5f1f4b8ad14</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/166bcfb1621840255ee24502d9b3c397ccfe9cb2">166bcfb1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:50:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream changed build system to flit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/da905035419937ea317602d544ff2b8a3971e116">da905035</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:50:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/726d004ce0a8e4932ebc538f736f4b43422ab217">726d004c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T00:54:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: Annotate python3-numpy and python3-pytest with <!nocheck>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/80849f1a29905c8532a38c5070f76e46a7d67def">80849f1a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T01:00:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Copy tests dir from source, test with installed package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/57e21ca6a831fb6c978fc2f040a6cc7b19423ef7">57e21ca6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T01:01:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add "Testsuite: autopkgtest-pkg-python"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-scitrack/-/commit/f945334a33fcb84367807af5c57454485e504f11">f945334a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-09T01:06:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6b9c6782d59be7c3d669b9e78328b8c384296d32">
.github/workflows/testing_develop.yml
</a>
</li>
<li class="file-stats">
<a href="#fc1a47a75cc8dc593b20b5e840173df634b008a1">
.hgtags
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
pyproject.toml
</a>
</li>
<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
<span class="deleted-file">
−
setup.cfg
</span>
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
<span class="deleted-file">
−
setup.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#7be999601ee10ece4542da6f9b045dc1b3346ebe">
src/scitrack/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#f996b3e9eb4ba2cf1c9808f7dfe45b052f75a9c6">
tests/test_logging.py
</a>
</li>
<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6b9c6782d59be7c3d669b9e78328b8c384296d32">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#6b9c6782d59be7c3d669b9e78328b8c384296d32"><strong>.github/workflows/testing_develop.yml</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ jobs:</td>
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<td class="old_line diff-line-num" 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">
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<td class="new_line diff-line-num" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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">
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<td class="new_line diff-line-num" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="17" 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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<td class="new_line diff-line-num old" data-linenumber="17" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="18" 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">
</td>
<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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 class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">3.9</span></span><span class="pi">]</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="25" 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">@@ -25,13 +25,13 @@ jobs:</td>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
</pre>
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<td class="old_line diff-line-num" 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">
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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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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m site</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" 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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<td class="new_line diff-line-num old" data-linenumber="28" 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="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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<td class="old_line diff-line-num new" data-linenumber="29" 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="new_line diff-line-num new" data-linenumber="28" 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="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install --upgrade pip setuptools wheel<span class="idiff left right"> flit</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="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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<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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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"></span>
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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 <span class="idiff left right">py3.8 </span>coverage to Codecov</span></span>
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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 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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<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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<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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@</td>
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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>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">d223af41764757c47b24f6594a4597818f18e785 2020.6.5</span></pre>
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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">@@ -66,6 +66,10 @@ Creating the logger. Setting ``create_dir=True`` means on creation of the logfil</td>
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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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.. warning::</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> Once set, a loggers ``.log_file_path`` cannot be changed.</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">******************************************</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">Capturing a programs arguments and options</span>
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<pre style="margin: 0;"> <span id="LC75" 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">@@ -74,6 +78,10 @@ Capturing a programs arguments and options</td>
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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="LC79" class="line" lang="plaintext">Here's one approach to incorporating ``scitrack`` into a command line application built 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="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.. note::</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.log_args()`` should be called immediately after the function definition, or after "true" default values have been configured.</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="LC85" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> import click</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="145" 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">@@ -137,4 +145,20 @@ Reporting issues</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC146" 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="LC147" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">**************</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">For Developers</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">**************</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">We use flit_ for package building. Having cloned the repository onto your machine. Install ``flit``::</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">$ python3 -m pip install flit</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">Do a developer install of ``scitrack`` using flit as::</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">$ cd path/to/cloned/repo</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">$ flit install -s --python `which python`</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">.. note:: This installs a symlink into ``site-packages`` of the python identified by ``which python``.</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">.. [1] The hexdigest serves as a unique signature of a files contents.</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.. _flit: https://flit.readthedocs.io/en/latest/</span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-scitrack (2021.5.3-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2021.5.3</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/watch: Fix watch regex</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * d/control: Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Upstream changed build system to flit</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> - d/rules: Declare PYBUILD_SYSTEM=flit</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - d/control: Add B-D on flit</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Improve testing</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> - d/control: Annotate python3-numpy and python3-pytest</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> with <!nocheck></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> - d/tests/run-unit-test: Copy tests dir from source, test</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> with installed package rather on the source directory where</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> upstream files are present</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> - d/control: Add "Testsuite: autopkgtest-pkg-python"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Mon, 09 Aug 2021 01:03:39 +0530</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="LC19" class="line" lang="plaintext">python-scitrack (2020.6.5-1) unstable; urgency=medium</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"> * New upstream version 2020.6.5</span>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -2,14 +2,16 @@ Source: python-scitrack</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>, Nilesh Patra <nilesh@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> flit,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python3-pytest,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-numpy</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-pytest<span class="idiff left right"> <!nocheck></span>,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-numpy<span class="idiff left right"> <!nocheck></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-scitrack</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-scitrack.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/HuttleyLab/scitrack</span>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export PYBUILD_NAME=scitrack</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export PYBUILD_SYSTEM=flit</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @, python3-all, python3-pytest, python3-numpy</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">CUR_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>py <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span>py3versions <span class="nt" style="color: #000080;">-r</span> 2> /dev/null<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/tests <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>py <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span>py3versions <span class="nt" style="color: #000080;">-s</span> 2> /dev/null<span class="si" style="color: #d14;">)</span></span>
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5
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"> <span class="nv" style="color: #008080;">$py</span> <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span></span>
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7
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/HuttleyLab/scitrack/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/HuttleyLab/scitrack/releases .*/archive/<span class="idiff left right">.*/</span>v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#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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<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;">"flit_core >=2,<4"</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;">"flit_core.buildapi"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="toml"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.flit.metadata]</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="toml"><span class="py">module</span> <span class="p">=</span> <span class="s" style="color: #d14;">"scitrack"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="toml"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">"Gavin Huttley"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="toml"><span class="py">author-email</span> <span class="p">=</span> <span class="s" style="color: #d14;">"Gavin.Huttley@anu.edu.au"</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="toml"><span class="py">home-page</span> <span class="p">=</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="toml"><span class="py">license</span> <span class="p">=</span> <span class="s" style="color: #d14;">"BSD-3"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="toml"><span class="py">description-file</span> <span class="p">=</span> <span class="s" style="color: #d14;">"README.rst"</span></span>
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<td class="new_line diff-line-num new" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="toml"><span class="py">keywords</span> <span class="p">=</span> <span class="s" style="color: #d14;">"science, logging"</span></span>
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<td class="new_line diff-line-num new" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="toml"><span class="py">classifiers</span> <span class="p">=</span> <span class="p">[</span></span>
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<td class="new_line diff-line-num new" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="toml"> <span class="s" style="color: #d14;">"Development Status :: 4 - Beta"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" 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="new_line diff-line-num new" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="toml"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" 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="new_line diff-line-num new" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="toml"> <span class="s" style="color: #d14;">"License :: OSI Approved :: BSD License"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="toml"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" 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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="toml"> <span class="s" style="color: #d14;">"Topic :: Software Development :: Libraries :: Python Modules"</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="toml"> <span class="s" style="color: #d14;">"Operating System :: OS Independent"</span><span class="p">,</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;">"Programming Language :: Python :: 3.6"</span><span class="p">,</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="toml"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.7"</span><span class="p">,</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="toml"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.8"</span><span class="p">,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="toml"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.9"</span><span class="p">,</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="toml"> <span class="p">]</span></span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="toml"><span class="py">requires-python</span> <span class="p">=</span> <span class="s" style="color: #d14;">">=3.6"</span></span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="toml"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.flit.sdist]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="toml"><span class="py">include</span> <span class="p">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"src/*"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pyproject.toml"</span><span class="p">,</span> <span class="s" style="color: #d14;">"*.rst"</span><span class="p">]</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="toml"><span class="py">exclude</span> <span class="p">=</span> <span class="nn" style="color: #555;">["*.xml"]</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="toml"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="toml"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.flit.metadata.urls]</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="toml"><span class="py">Documentation</span> <span class="p">=</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="toml"><span class="err" style="color: #a61717; background-color: #e3d2d2;">"Bug</span> <span class="py">Tracker"</span> <span class="p">=</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack/issues"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="toml"><span class="err" style="color: #a61717; background-color: #e3d2d2;">"Source</span> <span class="py">Code"</span> <span class="p">=</span> <span class="s" style="color: #d14;">"https://github.com/HuttleyLab/scitrack"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="toml"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.flit.metadata.requires-extra]</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="toml"><span class="py">test</span> <span class="p">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="toml"> <span class="s" style="color: #d14;">"black"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="toml"> <span class="s" style="color: #d14;">"isort"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="toml"> <span class="s" style="color: #d14;">"pytest"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="toml"> <span class="s" style="color: #d14;">"pytest-cov"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="toml"> <span class="s" style="color: #d14;">"tox"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="toml"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.black]</span></span>
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<pre style="margin: 0;"> <span id="LC46" 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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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">[bdist_wheel]</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">universal = 1</span></pre>
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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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2
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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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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;">sys</span></span>
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4
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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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6
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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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<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 2016-2020, Gavin Huttley"</span></span>
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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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<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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<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;">"2020.6.5"</span></span>
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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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<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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<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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<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="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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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">readme_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathlib</span><span class="p">.</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 class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"README.rst"</span></span>
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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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<pre style="margin: 0;">-<span id="LC40" 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 class="p">,</span></span>
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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="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="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="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/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#7be999601ee10ece4542da6f9b045dc1b3346ebe"><strong>src/scitrack/__init__.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">SciTrack provides basic logging capabilities to track scientific computations.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hashlib</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;">importlib</span></span>
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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;">inspect</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">@@ -11,10 +14,10 @@ from getpass import getuser</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" 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="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 2016-202<span class="idiff left right">0</span>, Gavin Huttley"</span></span>
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<pre style="margin: 0;">+<span id="LC17" 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 2016-202<span class="idiff left right">1</span>, Gavin Huttley"</span></span>
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<pre style="margin: 0;"> <span id="LC18" 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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<pre style="margin: 0;"> <span id="LC19" 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="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;">"202<span class="idiff left right">0.6.5</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC20" 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;">"202<span class="idiff left right">1.5.3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC21" 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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<pre style="margin: 0;"> <span id="LC22" 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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<pre style="margin: 0;"> <span id="LC23" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,6 +115,11 @@ class CachingLogger(object):</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log_file_path</span><span class="p">.</span><span class="n" style="color: #333;">setter</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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 class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">"""set the log file path and then dump cached log messages"""</span></span>
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<pre style="margin: 0;">+<span id="LC118" 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;">_log_file_path</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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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"log_file_path already defined as </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_file_path</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" 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;">create_dir</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC125" 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;">os</span><span class="p">.</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="n" style="color: #333;">path</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" 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="290" 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">@@ -282,11 +290,12 @@ def get_text_hexdigest(data):</td>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;"> 'rb' versus 'r' modes.</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC292" 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="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fmt: off</span></span>
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<pre style="margin: 0;"> <span id="LC294" 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="sa">u</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>
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295
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<pre style="margin: 0;"> <span id="LC295" 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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287
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296
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<pre style="margin: 0;"> <span id="LC296" 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="sa">b</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>
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288
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297
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<pre style="margin: 0;"> <span id="LC297" 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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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;"># fmt: on</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;">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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291
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300
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<pre style="margin: 0;"> <span id="LC300" 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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292
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301
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<pre style="margin: 0;"> <span id="LC301" 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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<li id="f996b3e9eb4ba2cf1c9808f7dfe45b052f75a9c6">
<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#f996b3e9eb4ba2cf1c9808f7dfe45b052f75a9c6"><strong>tests/test_logging.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -18,10 +18,10 @@ from scitrack import (</td>
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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="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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<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 2016-202<span class="idiff left right">0</span>, Gavin Huttley"</span></span>
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21
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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 2016-202<span class="idiff left right">1</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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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="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;">"202<span class="idiff left right">0.6.5</span>"</span></span>
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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;">"202<span class="idiff left right">1.5.3</span>"</span></span>
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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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<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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<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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,6 +47,18 @@ def test_creates_path():</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>
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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_set_path_if_exists</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;">"""cannot change an existing logging path"""</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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="s" style="color: #d14;">"."</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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<pre style="margin: 0;">+<span id="LC53" 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;">Path</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="LC54" 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="LC55" 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;">dirname</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">LOGFILE_NAME</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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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<pre style="margin: 0;">+<span id="LC57" 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;">AttributeError</span><span class="p">):</span></span>
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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;">dirname</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"invalid.log"</span></span>
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<pre style="margin: 0;">+<span id="LC59" 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="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC62" 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="LC63" 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="LC64" 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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<a href="https://salsa.debian.org/med-team/python-scitrack/-/compare/e44ae3eaed83fdead1ba1f72c59421b6e4e4331b...f945334a33fcb84367807af5c57454485e504f11#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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">isolated_build</span> <span class="p">=</span> <span class="s" style="color: #d14;">True</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">py36, py37, py38, py39</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="ini"></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv]</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">passenv</span> <span class="p">=</span> <span class="s" style="color: #d14;">*</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">@@ -8,6 +9,12 @@ deps = numpy</td>
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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</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest-cov</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="ini"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:py39]</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">changedir</span> <span class="p">=</span> <span class="s" style="color: #d14;">tests</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.9</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" 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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="ini"></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:py38]</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" 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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20
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<pre style="margin: 0;"> <span id="LC20" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="38" 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">@@ -31,3 +38,4 @@ python =</td>
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38
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<pre style="margin: 0;"> <span id="LC38" 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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39
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<pre style="margin: 0;"> <span id="LC39" 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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40
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<pre style="margin: 0;"> <span id="LC40" 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>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3.9:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">py39</span></span></pre>
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