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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/scrm">Debian Med / scrm</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e">cc548284</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T22:03:40+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.7.4</pre>
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<h4>11 changed files:</h4>
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<a href="#6e656a06857650151f28f253233ed97584044098">
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+
.devcontainer/Dockerfile
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<li class="file-stats">
<a href="#b34062a34eb177d6796c9ce334de4930d86f38c1">
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.devcontainer/devcontainer.json
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#8e91c39ea457744ee86e8378b154b7f3bb28e325">
NEWS.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#a9c47e9dc92869413b59ebeaeb245b6061e12f4e">
src/forest.cc
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<li class="file-stats">
<a href="#a127a6b5c4d7c6af14b0c3e1763b7840725fdd58">
src/param.cc
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<li class="file-stats">
<a href="#f34bf61081d325b0254a85c1dfe0a0cead3dc9a6">
tests/test_binaries.sh
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<li class="file-stats">
<a href="#b67a9d836fdc1c21d463c6f24bcc629018ee27ab">
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+
tests/tree.newick
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<h4>Changes:</h4>
<li id="6e656a06857650151f28f253233ed97584044098">
<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#6e656a06857650151f28f253233ed97584044098"><strong>.devcontainer/Dockerfile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> debian:buster-slim</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="docker"> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="docker"> autoconf <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="docker"> autoconf-archive <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"> automake <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"> build-essential <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="docker"> git <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="docker"> libcppunit-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"> valgrind <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"> apt-get clean <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</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="docker"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /var/lib/apt/lists/ <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</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="docker"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /tmp/downloaded_packages/ /tmp/<span class="k" style="font-weight: 600;">*</span>.rds </span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="docker"></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>adduser developer</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"></span>
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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="docker"><span class="k" style="font-weight: 600;">USER</span><span class="s" style="color: #d14;"> developer</span></span></pre>
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<li id="b34062a34eb177d6796c9ce334de4930d86f38c1">
<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#b34062a34eb177d6796c9ce334de4930d86f38c1"><strong>.devcontainer/devcontainer.json</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">For</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">format</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">details,</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">see</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">https://aka.ms/vscode-remote/devcontainer.json</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">or</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">this</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">file's</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">README</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">at:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="json"><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">https://github.com/microsoft/vscode-dev-containers/tree/v</span><span class="mf" style="color: #099;">0.101</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="mi" style="color: #099;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/containers/docker-existing-dockerfile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"scrm:develop"</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="json"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Sets</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">run</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">context</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">one</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">level</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">up</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">instead</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">of</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.devcontainer</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">folder.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"context"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"."</span><span class="p">,</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Update</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">'dockerFile'</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">property</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">you</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">aren't</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">using</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">standard</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">'Dockerfile'</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">filename.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"dockerFile"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Dockerfile"</span><span class="p">,</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Set</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">*default*</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">specific</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">settings.json</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">values</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">on</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">create.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"settings"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="w" style="color: #bbb;"> </span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"terminal.integrated.shell.linux"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">null</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Add</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">IDs</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">of</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">extensions</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">you</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">want</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">installed</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">when</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">is</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">created.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"extensions"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"ms-vscode.cpptools"</span><span class="p">],</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="json"></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Use</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">'forwardPorts'</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">a</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">list</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">of</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">ports</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">inside</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">available</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">locally.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="nl">"forwardPorts"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[],</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Uncomment</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">next</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">line</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">run</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">commands</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">after</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">is</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">created</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">example</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">installing</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">git.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="nl">"postCreateCommand"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"apt-get update && apt-get install -y git"</span><span class="p">,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="json"></span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Uncomment</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">when</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">using</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">a</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">ptrace-based</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">debugger</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">like</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">C++</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Go</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">and</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Rust</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="nl">"runArgs"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"--cap-add=SYS_PTRACE"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"--security-opt"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"seccomp=unconfined"</span><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="json"></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Uncomment</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">use</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Docker</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">CLI</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">from</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">inside</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">the</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">container.</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">See</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">https://aka.ms/vscode-remote/samples/docker-in-docker.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="nl">"mounts"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind"</span><span class="w" style="color: #bbb;"> </span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="json"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Uncomment</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">connect</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">as</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">a</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">non-root</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">user.</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">See</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">https://aka.ms/vscode-remote/containers/non-root.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"remoteUser"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"developer"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="json"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</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">@@ -36,6 +36,7 @@ tests/*working*</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">scrm</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">scrm_dbg</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">scrm_prof</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">scrm_asan</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"># automake</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Makefile</span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.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">@@ -13,7 +13,7 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC13" 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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CXXFLAGS="-m32 -Werror"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">xenial</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">bionic</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span> <span class="s" style="color: #d14;">.travis/setup.sh "$TRAVIS_OS_NAME" "$CXX" "$CXXFLAGS"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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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;">./bootstrap</span></span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#8e91c39ea457744ee86e8378b154b7f3bb28e325"><strong>NEWS.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">scrm Version History</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========================</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">scrm 1.7.4</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">Released: 2020-03-07</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">+</span> Fixes the initialization with an inital tree in Newick format (<span class="sb" style="color: #d14;">`-init`</span>).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"> Big thanks to @nspope for reporting and locating this bug along with</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"> suggesting a fix! </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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4
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="gh" style="color: #999;">scrm 1.7.3</span></span>
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5
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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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------</span></span>
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6
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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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">Released: 2018-11-18</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Project Status: <span class="idiff left">Active - The project has reached a stable, usable state and is being actively developed.</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://www.repostatus.org/badges/latest/active.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](http://www.repostatus.org/#</span>active)</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Project Status: <span class="idiff left">Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://www.repostatus.org/badges/latest/inactive.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://www.repostatus.org/#in</span>active)</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" 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.org/scrm/scrm.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/scrm/scrm)</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="markdown"></span>
</pre>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">scrm</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="45" 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">@@ -45,8 +45,7 @@ Details are available [in the wiki][2].</td>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Troubleshooting</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown">If you encounter problems while using _scrm_, please </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">file a bug report</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/scrm/scrm/wiki/Reporting-Bugs</span><span class="p">)</span> or mail to</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="sb" style="color: #d14;">`develop (at) paulstaab.de`</span>.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">file a bug report</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/scrm/scrm/wiki/Reporting-Bugs</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT([scrm], [1.7.<span class="idiff left right">3</span>],[https://github.com/paulstaab/scrm/issues])</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT([scrm], [1.7.<span class="idiff left right">4</span>],[https://github.com/paulstaab/scrm/issues])</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects -Wall -Werror foreign])</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># Use -O3 as default optimization level</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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>
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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">@@ -52,6 +52,7 @@ AX_CHECK_COMPILE_FLAG([-Wcast-align], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wcast-align"</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">AX_CHECK_COMPILE_FLAG([-Wunused], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wunused"], [], [-Werror])</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">AX_CHECK_COMPILE_FLAG([-Woverloaded-virtual], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Woverloaded-virtual"], [], [-Werror])</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">AX_CHECK_COMPILE_FLAG([-pedantic], [OPT_CXXFLAGS="$OPT_CXXFLAGS -pedantic"], [], [-Werror])</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">AX_CHECK_COMPILE_FLAG([-Wcatch-value], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wcatch-value"], [], [-Werror])</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">AC_CONFIG_FILES([Makefile])</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">AC_OUTPUT</span></pre>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#a9c47e9dc92869413b59ebeaeb245b6061e12f4e"><strong>src/forest.cc</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">@@ -1324,7 +1324,8 @@ Node* Forest::readNewickNode( std::string &in_str, std::string::iterator &it, si</td>
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Forest</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">readNewick</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">in_str</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC1327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_rec_</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_next_base</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">current_rec_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_str</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="cpp"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readNewickNode</span><span class="p">(</span> <span class="n" style="color: #333;">in_str</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_local_root</span><span class="p">(</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nodes</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">last</span><span class="p">()</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#a127a6b5c4d7c6af14b0c3e1763b7840725fdd58"><strong>src/param.cc</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">@@ -132,7 +132,7 @@ Model Param::parse() {</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there might or might not follow a symmetric migration rate</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">addSymmetricMigration</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">readNextInput</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">population_number</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">argv_i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="p">}</span></span>
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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">@@ -382,7 +382,7 @@ Model Param::parse() {</td>
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Maybe read in up to 3 seeds (ms compatibility)</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readNextInt</span><span class="p">();</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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386
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">argv_i</span><span class="p">;</span></span>
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387
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="p">}</span></span>
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388
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#f34bf61081d325b0254a85c1dfe0a0cead3dc9a6"><strong>tests/test_binaries.sh</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">@@ -13,6 +13,7 @@ make scrm_asan 2> /dev/null</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">supports_sanitizers</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$?</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$supports_sanitizers</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></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;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Using address sanitizers"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">ASAN_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">detect_leaks</span><span class="o" style="font-weight: 600;">=</span>0</span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>test_scrm <span class="o" style="font-weight: 600;">{</span></span>
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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">@@ -60,6 +61,7 @@ echo "Testing Initial Tree"</td>
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60
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"> test_scrm 25 1 <span class="nt" style="color: #000080;">-T</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"> test_scrm 10 5 <span class="nt" style="color: #000080;">-I</span> 1 5 <span class="nt" style="color: #000080;">-eI</span> 1.0 5 <span class="nt" style="color: #000080;">-L</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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62
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"> test_scrm 10 5 <span class="nt" style="color: #000080;">-I</span> 2 2 2 0.5 <span class="nt" style="color: #000080;">-eI</span> 1.0 3 3 <span class="nt" style="color: #000080;">-L</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> test_scrm 3 1 <span class="nt" style="color: #000080;">-init</span> tests/tree.newick <span class="nt" style="color: #000080;">-t</span> 5 <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing Recombinations"</span></span>
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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">@@ -67,6 +69,7 @@ echo "Testing Recombinations"</td>
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67
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"> test_scrm 6 10 <span class="nt" style="color: #000080;">-r</span> 1 100 <span class="nt" style="color: #000080;">-t</span> 5 <span class="nt" style="color: #000080;">-L</span> <span class="nt" style="color: #000080;">-T</span> <span class="nt" style="color: #000080;">-transpose-segsites</span> <span class="nt" style="color: #000080;">-l</span> <span class="nt" style="color: #000080;">-1</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"> test_scrm 8 10 <span class="nt" style="color: #000080;">-r</span> 1 100 <span class="nt" style="color: #000080;">-t</span> 5 <span class="nt" style="color: #000080;">-oSFS</span> <span class="nt" style="color: #000080;">-O</span> <span class="nt" style="color: #000080;">-l</span> <span class="nt" style="color: #000080;">-1</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"> test_scrm 10 5 <span class="nt" style="color: #000080;">-r</span> 5 100 <span class="nt" style="color: #000080;">-I</span> 2 2 2 0.5 <span class="nt" style="color: #000080;">-eI</span> 1.0 3 3 <span class="nt" style="color: #000080;">-L</span> <span class="nt" style="color: #000080;">-l</span> <span class="nt" style="color: #000080;">-1</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="diff-line-num new old_line" data-linenumber="70" 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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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> test_scrm 3 10 <span class="nt" style="color: #000080;">-r</span> 5 100 <span class="nt" style="color: #000080;">-init</span> tests/tree.newick <span class="nt" style="color: #000080;">-t</span> 5 <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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70
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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72
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing Pruning"</span></span>
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<a href="https://salsa.debian.org/med-team/scrm/-/commit/cc548284c3c74e876b25d3dfc71dade84a5c339e#b67a9d836fdc1c21d463c6f24bcc629018ee27ab"><strong>tests/tree.newick</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">((1:1.0,2:1.0):1.0,3:1.0);</span></pre>
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