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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch upstream at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/augur/-/commit/4711f710cdcf0a71c4a7ec0ac57a74c42bc08d27">4711f710</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2024-01-30T20:30:43+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "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 24.0.0</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<a href="#a91b1970808e533a5de67f93824231e12770a765">
.github/workflows/ci.yaml
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<a href="#3679a14291455b741a3f8e4314b4280f29f3c0ff">
.github/workflows/release.yaml
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<a href="#56d8f25ba935afb0dcf8e3343d57ad79897efb33">
.github/workflows/sync-redirects.yaml
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<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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DEPRECATED.md
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<a href="#69f17ab31be5979667265a94a4d0ec2749588bd4">
augur/__init__.py
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<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.py
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<a href="#73daf62265fd7608625d8a35b16297aed2a2399e">
augur/ancestral.py
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<a href="#75dd11b179bed0c75a7e63134345d60a147c6525">
augur/data/lat_longs.tsv
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<a href="#7051dc1354d6bc0d4b68367cda18a5846f82adb6">
augur/export_v2.py
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augur/filter/include_exclude_rules.py
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<a href="#2c0e8e80cc69382c40326b05bc7e76ca7fd787bb">
augur/io/__init__.py
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augur/io/strains.py
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augur/translate.py
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<a href="#0d0305472fcbc5cf656b5d71a25dfd30c8c8d131">
augur/utils.py
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<a href="#73cc809ba2916206462a7eb6005867f214a34fcc">
docs/contribute/DEV_DOCS.md
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docs/releases/DEPRECATED.md
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docs/releases/breaking.md
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<a href="#e729e70b9370f1895bde254d944c1d02435fa586">
docs/releases/releases.rst
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<a href="#dd3600e7571652727b6b8ae37346a4a6e909564e">
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scripts/compare-json-vcf.py
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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tests/functional/ancestral/cram/ambiguous-positions.t
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tests/functional/ancestral/cram/case-sensitive.t
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tests/functional/ancestral/cram/general.t
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tests/functional/ancestral/cram/infer-amino-acid-sequences-genes-file.t
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tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
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tests/functional/ancestral/cram/invalid-args.t
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tests/functional/ancestral/cram/vcf-multi-allele.t
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tests/functional/ancestral/cram/vcf.t
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tests/functional/ancestral/data/genes.txt
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
</h5>

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