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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/48be2431c2df6cb6d111f1d14b4fafa67d135450">48be2431</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-17T09:49:12+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.30.4</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6cd2a502257ede524d220cea6700e2fa98f071aa">
.github/workflows/wheels.yml
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#2fbcc692367300b0691462028f2e5f9bcaaf0945">
cyvcf2/__init__.py
</a>
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<h4>Changes:</h4>
<li id="6cd2a502257ede524d220cea6700e2fa98f071aa">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/48be2431c2df6cb6d111f1d14b4fafa67d135450#6cd2a502257ede524d220cea6700e2fa98f071aa"><strong>.github/workflows/wheels.yml</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">@@ -54,3 +54,37 @@ jobs:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">./wheelhouse/*.whl</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">build_sdist</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build source distribution</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install Python</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build sdist</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python setup.py sdist</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/*.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">upload_pypi</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">build_wheels</span><span class="pi">,</span> <span class="nv" style="color: #008080;">build_sdist</span><span class="pi">]</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># upload to PyPI on every tag starting with 'v'</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/download-artifact@v2</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">artifact</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/gh-action-pypi-publish@master</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">__token__</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.PYPI_API_TOKEN }}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/48be2431c2df6cb6d111f1d14b4fafa67d135450#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -13,7 +13,8 @@ If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformati</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">Fast python <span class="gs" style="font-weight: 600;">**(2 and 3)**</span> parsing of VCF and BCF including region-queries.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.com/brentp/cyvcf2.svg?branch=master</span><span class="p">)</span>](https://travis-ci.com/brentp/cyvcf2)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/cyvcf2/workflows/Build/badge.svg</span><span class="p">)</span>](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">cyvcf2 is a cython wrapper around <span class="p">[</span><span class="nv" style="color: #008080;">htslib</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/samtools/htslib</span><span class="p">)</span> built for fast parsing of <span class="p">[</span><span class="nv" style="color: #008080;">Variant Call Format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.m.wikipedia.org/wiki/Variant_Call_Format</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">VCF</span><span class="p">)</span> files.</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/48be2431c2df6cb6d111f1d14b4fafa67d135450#2fbcc692367300b0691462028f2e5f9bcaaf0945"><strong>cyvcf2/__init__.py</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">@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="n" style="color: #333;">par_het</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCFReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.<span class="idiff left right">2</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.<span class="idiff left right">4</span>"</span></span></pre>
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