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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/gubbins">Debian Med / gubbins</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/8ed57cf96e71e00ace67702e586053f35286b036">8ed57cf9</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T18:36:38+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 3.4</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/cbd588e7747e9dcbeeea3d7dadae4f4027d24830">cbd588e7</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T18:36:49+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/3.4'
Update to upstream version '3.4'
with Debian dir d153bfc6d870f71689114e396162e5abce1d2fb8</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/402305b38d3982851eecd7603a0f440c1ebc5209">402305b3</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T18:44:05+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/copyright: document missing copyright owners.
Those are Wellcome Trust Sanger Institute and Imperial College London.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/7a1a646438caa5ccf4eb14c9de562683cb49dc42">7a1a6464</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T18:57:00+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: declare compliance to standards version 4.7.0.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/65b0968783423cc7e642e0a696e1dfb6650ed9fe">65b09687</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T18:58:49+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/patches/*: normalise last-update timestamp to dep3.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/ed2d2ea4d007e24f13e667ea8b0b404499bddc95">ed2d2ea4</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-11-30T19:00:31+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/changelog: ready for upload to unstable.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
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<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
.github/workflows/build.yml
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<li class="file-stats">
<a href="#1cddcc9805216c16db371e61f0c564291a4c4f0a">
R/scripts/plot_gubbins.R
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#c26ef0f252effd52e649af2d8504feb2e54df0b0">
debian/patches/autoupdate_configure.ac.patch
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<li class="file-stats">
<a href="#60c7f35251e97e6e084e0ac6c78e80addff1beb9">
debian/patches/do_not_handle_python_by_upstream_build_system.patch
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<li class="file-stats">
<a href="#3a2470b33ad88916745979351435ccba0d2f1100">
debian/patches/gubbins_exe_in_usr_lib.patch
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<li class="file-stats">
<a href="#15ccbf0b31b48daaa7c2f3dd64a91bcb9322dc4c">
debian/patches/iqtree2.patch
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<li class="file-stats">
<a href="#bafdb3502355421f7d2baba654f27b2d08fce881">
docs/gubbins_manual.md
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<li class="file-stats">
<a href="#aaaba74cad9a3f815206ba8bf91e26f24eb5a22a">
python/gubbins/common.py
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<li class="file-stats">
<a href="#8b162ca414f3ac3d2cc363c44968e6d4061354ac">
python/gubbins/tests/test_python_scripts.py
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<li class="file-stats">
<a href="#5c2480d22d89c2d40195404d58ebb2c2e2755aeb">
python/gubbins/tests/test_utils.py
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</li>
<li class="file-stats">
<a href="#b37728bccd07a22008bf25dd8e4521fc8d157087">
python/gubbins/treebuilders.py
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</li>
<li class="file-stats">
<a href="#0452b1f8c4d2a44bb544f6ac29fc88719de5614e">
python/gubbins/utils.py
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<li class="file-stats">
<a href="#7aaaebcf27a2838cd5f972eb2c685c96ed11aa39">
<span class="new-file">
+
python/scripts/extract_recombinant_sequences.py
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</li>
<li class="file-stats">
<a href="#736ae1bee457a1fb132cee635e1205a31bf0f0a5">
python/scripts/generate_ska_alignment.py
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<li class="file-stats">
<a href="#fc5fcc005fd16db919d0efc12a031869967a9872">
python/setup.py
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<li class="file-stats">
<a href="#17136e44e5940083fc2b5c86767caca042ae8818">
src/Newickform.c
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<li class="file-stats">
<a href="#f06b916d84aa243d5f3e46ad8c4a917e5c3a616e">
src/Newickform.h
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<li class="file-stats">
<a href="#fd7720ed03d136357a86f5b86ddc39632eb5d8b5">
src/block_tab_file.c
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<li class="file-stats">
<a href="#b3728d6b8dd7bbe0282e3f09d571eb07bcfa076d">
src/branch_sequences.c
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<li class="file-stats">
<a href="#781b51ac2c785a73c42190283ec13205c20e2ae2">
src/branch_sequences.h
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<li class="file-stats">
<a href="#a07e3b331cc2fef355ec6147fa39381590d55f1f">
src/csv_of_snp_sites.c
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<li class="file-stats">
<a href="#80d45c8775ba36adf3ee43ca9dcb40402f565a06">
src/gubbins.c
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<li class="file-stats">
<a href="#ba8ff0dd6ad6a8708a879e0b570aa1ef122b0690">
src/gubbins.h
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<li class="file-stats">
<a href="#3a576e09615c0e19842e5f3ac31e858c9ae7fe41">
src/main.c
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
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—
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<a href="https://salsa.debian.org/med-team/gubbins/-/compare/84c753717101b71a990a4ee96100543f720a749f...ed2d2ea4d007e24f13e667ea8b0b404499bddc95">View it on GitLab</a>.
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