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<h3>
Nilesh Patra 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/5a8626a17c03e2818a9e2868adc6337274d65847">5a8626a1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-04T19:57:41+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.30.0</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#f9914cb1e6160c44a380b12482a808b27e0fe7ec">
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+
ci/linux-deps
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<li class="file-stats">
<a href="#46db7d66bb4749507715f43937a38090669cecfb">
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+
ci/osx-deps
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<li class="file-stats">
<a href="#2429c55be0b59762a008ba672354b0d0ae1358a9">
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+
ci/test
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<li class="file-stats">
<a href="#2fbcc692367300b0691462028f2e5f9bcaaf0945">
cyvcf2/__init__.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/5a8626a17c03e2818a9e2868adc6337274d65847#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<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">@@ -7,10 +7,15 @@ python:</td>
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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="yaml"> <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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<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="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" 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="9" 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="LC9" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">homebrew</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">openssl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="16" 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="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install libcurl4-openssl-dev</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" 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="17" 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="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -r requirements.txt</span></span>
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<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd htslib</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="18" 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="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd htslib</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="19" 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="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">autoheader && autoconf</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./configure --enable-s3 --disable-lzma --disable-bz2</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="24" 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">@@ -19,3 +24,49 @@ install:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py test</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</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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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_SKIP="pp* cp27-* cp34-* *i686*"</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_BEFORE_BUILD_LINUX="{project}/ci/linux-deps"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_TEST_COMMAND="{project}/ci/test"</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_ENVIRONMENT="CYTHONIZE=1 LDFLAGS='-L/usr/lib64/openssl11' CPPFLAGS='-I/usr/include/openssl11' C_INCLUDE_PATH='/root/include' LIBRARY_PATH='/root/lib'"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">services</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3 -m pip install cibuildwheel</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3 -m cibuildwheel --output-dir wheelhouse</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ "${TRAVIS_TAG:-}" != "" ]; then</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m pip install twine -U</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload --repository testpypi --skip-existing wheelhouse/*</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 setup.py sdist</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload --repository testpypi --skip-existing dist/*</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode10.2</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">shell</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_SKIP="pp* cp27-* cp34-* *i686*"</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_BEFORE_BUILD_MACOS="{project}/ci/osx-deps"</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_TEST_COMMAND="{project}/ci/test"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CIBW_ENVIRONMENT="CYTHONIZE=1"</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">LDFLAGS="-L/usr/local/opt/openssl@1.1/lib"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CPPFLAGS="-I/usr/local/opt/openssl@1.1/include"</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">PKG_CONFIG_PATH="/usr/local/opt/openssl@1.1/lib/pkgconfig"</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3 -m pip install cibuildwheel</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3 -m cibuildwheel --output-dir wheelhouse</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ "${TRAVIS_TAG:-}" != "" ]; then</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m pip install twine -U</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload --repository testpypi --skip-existing wheelhouse/*</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/5a8626a17c03e2818a9e2868adc6337274d65847#f9914cb1e6160c44a380b12482a808b27e0fe7ec"><strong>ci/linux-deps</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">yum <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> openssl11-devel</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell">yum <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> libffi libffi-devel zlib-devel</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">yum <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> bzip2-devel bzip2-libs xz-devel xz-libs</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">python <span class="nt" style="color: #000080;">-m</span> pip <span class="nb" style="color: #0086b3;">install </span>pip <span class="nt" style="color: #000080;">--upgrade</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">git submodule init</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell">git submodule update</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-O</span> https://www.libssh2.org/download/libssh2-1.9.0.tar.gz</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xzf libssh2-1.9.0.tar.gz</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>libssh2-1.9.0</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">./configure <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span>/root</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">make</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">install</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> libssh2-1.9.0</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-O</span> https://curl.se/download/curl-7.73.0.tar.gz</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xzf curl-7.73.0.tar.gz</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>curl-7.73.0</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">./configure <span class="nt" style="color: #000080;">--with-libssh2</span> <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span>/root</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">make</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">install</span></span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> curl-7.73.0</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>htslib</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">autoheader</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">autoconf</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">./configure <span class="nt" style="color: #000080;">--enable-libcurl</span> <span class="nt" style="color: #000080;">--enable-s3</span> <span class="nt" style="color: #000080;">--enable-lzma</span> <span class="nt" style="color: #000080;">--enable-bz2</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">make</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-r</span> requirements.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/5a8626a17c03e2818a9e2868adc6337274d65847#46db7d66bb4749507715f43937a38090669cecfb"><strong>ci/osx-deps</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">python <span class="nt" style="color: #000080;">-m</span> pip <span class="nb" style="color: #0086b3;">install </span>pip <span class="nt" style="color: #000080;">--upgrade</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">git submodule init</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell">git submodule update</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>htslib</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">autoheader</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell">autoconf</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">./configure <span class="nt" style="color: #000080;">--enable-libcurl</span> <span class="nt" style="color: #000080;">--enable-s3</span> <span class="nt" style="color: #000080;">--enable-lzma</span> <span class="nt" style="color: #000080;">--enable-bz2</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">make</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-r</span> requirements.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/5a8626a17c03e2818a9e2868adc6337274d65847#2429c55be0b59762a008ba672354b0d0ae1358a9"><strong>ci/test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">cd</span> ~/ <span class="o" style="font-weight: 600;">&&</span> cyvcf2 <span class="nt" style="color: #000080;">--help</span> <span class="o" style="font-weight: 600;">></span>/dev/null<span class="o" style="font-weight: 600;">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"cyvcf2 --help: OK"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">cd</span> ~/ <span class="o" style="font-weight: 600;">&&</span> python <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"from cyvcf2 import VCF; VCF('https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz')"</span><span class="o" style="font-weight: 600;">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Remote reading: OK"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/5a8626a17c03e2818a9e2868adc6337274d65847#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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2
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2
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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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3
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3
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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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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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5
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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.<span class="idiff left right">20.9</span>"</span></span></pre>
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5
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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.<span class="idiff left right">30.0</span>"</span></span></pre>
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