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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/9a895eb6c6ce56eaaad7a4c706a53c085c20d605">9a895eb6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-07T17:07:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/07c541f8b7762d09d10e14263786f64f79a20c8e">07c541f8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-07T17:13:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">enlighten is now available
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/df6596ba74a539ff268aaa3ab27906c2fbd87214">df6596ba</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-07T17:13:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patch metadata
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
</a>
</li>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
debian/README.source
</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="#43bce5830afffd9cb2acc8dc5edc5294f813bf08">
debian/patches/debianize_docs
</a>
</li>
<li class="file-stats">
<a href="#e94fbb8719c4a68a67df894f2683205bb9914852">
debian/patches/no_galaxy_lib
</a>
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<li class="file-stats">
<a href="#e4edc1d4104bcf89de6479329e0a1f666d285d01">
debian/patches/no_virtualenv_to_create_manpages.patch
</a>
</li>
<li class="file-stats">
<a href="#162e41e7c3dcfdb5813c4718e3f8503d4861a8ba">
debian/patches/remove-pathlib2-dep
</a>
</li>
<li class="file-stats">
<a href="#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">
debian/patches/setting_version.patch
</a>
</li>
<li class="file-stats">
<a href="#c1fb0e9c942747a583cd8adc2707dd0cb1d97505">
debian/patches/soften-mesos-deps
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</li>
<li class="file-stats">
<a href="#cb805f74cef9b2dafa0758f976c0bcadda0b7dde">
debian/patches/version.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,4 +5,4 @@ This package is still preliminary since</td>
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> * testing is not activated</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * manpages are missing</span>
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<br>
</li>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,4 +7,4 @@ compatability of toil is recent.</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">The bulk of the manual testing is currently focused on the toil-cwl-runner</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext">using the docker.io package.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,9 +2,10 @@ toil (4.1.0-1) UNRELEASED; urgency=medium</td>
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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</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Refreshed the patches</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> TODO: package python3-enlighten</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Update patch metatdata</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="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>> Thu, 07 May 2020 15:00:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>> Thu, 07 May 2020 15:00:22 +0200</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">toil (4.0.0-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#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">@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Michael R. Crusoe <crusoe@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: net</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 (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</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"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</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">@@ -14,6 +14,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-pytest-xdist,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> cwltool,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3-distutils,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python3-enlighten,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># documentation</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python3-urllib3,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-sphinx</span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#43bce5830afffd9cb2acc8dc5edc5294f813bf08"><strong>debian/patches/debianize_docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Update docs to reflect a local install</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/index.rst</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/index.rst</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -31,7 +31,6 @@</span></span>
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<li id="e94fbb8719c4a68a67df894f2683205bb9914852">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#e94fbb8719c4a68a67df894f2683205bb9914852"><strong>debian/patches/no_galaxy_lib</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: skip galaxy-lib, not yet packaged for Debian</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -31,7 +31,6 @@</span></span>
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<li id="e4edc1d4104bcf89de6479329e0a1f666d285d01">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#e4edc1d4104bcf89de6479329e0a1f666d285d01"><strong>debian/patches/no_virtualenv_to_create_manpages.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: ignore requirement to use a virtualenv</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/conf.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/conf.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -36,8 +36,8 @@</span> def fetch_parent_dir(filepath, n=1):</span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#162e41e7c3dcfdb5813c4718e3f8503d4861a8ba"><strong>debian/patches/remove-pathlib2-dep</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: pathlib2 isn't needed for python3-toil</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -41,7 +41,6 @@</span></span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6"><strong>debian/patches/setting_version.patch</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">@@ -2,7 +2,7 @@ Description: Fixing version.py that is variable and required</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/851365</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 20<span class="idiff left right">18-06-14</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 20<span class="idiff left right">20-05-07</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">Generated by running `python version_template.py` from a git checkout of the</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">source to the tag corresponding to the release</span></span>
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<li id="c1fb0e9c942747a583cd8adc2707dd0cb1d97505">
<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#c1fb0e9c942747a583cd8adc2707dd0cb1d97505"><strong>debian/patches/soften-mesos-deps</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: Use Debian's newer python3-psutil</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Skip addict</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -41,7 +41,6 @@</span></span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/47569819244bbb35677703a5ed5953907e93384a...df6596ba74a539ff268aaa3ab27906c2fbd87214#cb805f74cef9b2dafa0758f976c0bcadda0b7dde"><strong>debian/patches/version.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: allow the use of Debian packaged dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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