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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pybedtools">Debian Med / python-pybedtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pybedtools/commit/b0752f36626fc7589f40f9b6960e722e3965c2d4">b0752f36</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-07-13T11:44:07+03:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add a patch to fix tests. Turn on testing
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#88da04ecb9d559c3540e9b9a3b38124d23bc842c">
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+
debian/patches/define_filenotfounderror_python2.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="88da04ecb9d559c3540e9b9a3b38124d23bc842c">
<a href="https://salsa.debian.org/med-team/python-pybedtools/commit/b0752f36626fc7589f40f9b6960e722e3965c2d4#88da04ecb9d559c3540e9b9a3b38124d23bc842c"><strong>debian/patches/define_filenotfounderror_python2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Liubov Chuprikova <chuprikovalv@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Wed, 13 July 2018 11:36:44 +0300</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Define FileNotFoundError as OSError for python 2</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pybedtools/test/test1.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pybedtools/test/test1.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20,6 +20,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import warnings</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FileNotFoundError</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except NameError:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # python2</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FileNotFoundError = OSError</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> def fix(x):</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pybedtools/contrib/bigwig.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pybedtools/contrib/bigwig.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6,6 +6,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> import subprocess</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FileNotFoundError</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except NameError:</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # python2</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FileNotFoundError = OSError</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> def mapped_read_count(bam, force=False):</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> """</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> Scale is cached in a bam.scale file containing the number of mapped reads.</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pybedtools/commit/b0752f36626fc7589f40f9b6960e722e3965c2d4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,3 +4,4 @@ disable-write-version</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">disable-test-156</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">rename-scripts</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">define_filenotfounderror_python2.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/python-pybedtools/commit/b0752f36626fc7589f40f9b6960e722e3965c2d4#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,5 +27,3 @@ override_dh_auto_install:</td>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> rm -fr debian/python-pybedtools/usr/bin</span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> rm -fr debian/python3-pybedtools/usr/bin</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">override_dh_auto_test:</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> echo "Not testing."</span></pre>
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