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<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch master at <a href="https://salsa.debian.org/med-team/toil" style="color: #1068bf;">Debian Med / toil</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/9631f696611afbbfa01c39f366b20bb9f676d224" style="color: #1068bf;">9631f696</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T15:57:42+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Fix watch file
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/8d5c635defdad60db05b60e83f88bac79f3e89a7" style="color: #1068bf;">8d5c635d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T15:57:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 5.7.1</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/c306fdc6208557b6c9fa4f62a6cb6654e2cb3a6f" style="color: #1068bf;">c306fdc6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T15:57:54+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/924093e36d86df3e9e0144c8e77683846abb8969" style="color: #1068bf;">924093e3</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T15:58:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/5.7.1'

Update to upstream version '5.7.1'
with Debian dir d0e257adfb38622ad4b0cf73c661c7fc488976ab</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/a4a8a8d6658d0c08f26001937ecd29d32c7d3c1b" style="color: #1068bf;">a4a8a8d6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T15:58:14+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.

Changes-By: lintian-brush
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/d3db6c9ef7b89851ac32e98731c5fa7f7d5a2da2" style="color: #1068bf;">d3db6c9e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T16:01:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Refresh patches
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/toil/-/commit/9e0c25719d2b45939e8c35f97e7bd866e2d1c633" style="color: #1068bf;">9e0c2571</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-06T16:08:16+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>TODO: NameError: name 'Object' is not defined
</pre>
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