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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libedlib">Debian Med / libedlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/047612d7318f8caa3b7e78d1fa2b2e15bd286a36">047612d7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:50:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/81add7e135537c10c2655f6f60504da02069fce9">81add7e1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/0648e0c336a3b4d3a4f2c20504b3a5e35d62ca84">0648e0c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/b1e88b3148f833120354c75e93cba67b11c34d1d">b1e88b31</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.7'
Update to upstream version '1.2.7'
with Debian dir de0d747e1d8347abcce9b17cbff637a90dd9151d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/b411cb3bbaaec1fb8b3ee671ac99c2cc6d218fa4">b411cb3b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/b729c8b59d33c36c14836ac90fcfc387a001081b">b729c8b5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/414830fedcdf1b4dd02cf67754e41d966135ead9">414830fe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/66ec0f9df19b1f0298b90cae50a9e2bc12fb398c">66ec0f9d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/34c2439f7ab5bb8b0e1d0e114605c73376bfcffd">34c2439f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/738a56327cc1175b62042e8d1d3623df651970ec">738a5632</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:51:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/b77c1b513f8f69cc0a90fa83faf29b677089b364">b77c1b51</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T11:52:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply multi-arch hints.
+ libedlib-dev, libedlib0, python3-edlib: Add Multi-Arch: same.
Changes-By: apply-multiarch-hints
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/5c9f8ff5646ab84a4ffa3638b8e8890d3b0515ad">5c9f8ff5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T12:05:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add filemangle
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/31195ebf7058a27fdeaf3acc338ab1e421e70c85">31195ebf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T12:16:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/35385321f6d8bac1fed7b9fba5169881bc1b70de">35385321</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:30:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Several things needs to be adjusted to build flawlessly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/53be7cbacd9b99987a3ac5480951ddb423e6e674">53be7cba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:31:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream decided to use SOVERSION 1 - so follow this decision
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/-/commit/9fe8873554cb4607bd8e8e864e2eb3db97f34761">9fe88735</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:40:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install cmake files
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<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="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<span class="new-file">
+
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#43b9d80d1f50472e56afb94a061257af5b53182b">
appveyor.yml
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<li class="file-stats">
<a href="#afbead18ab75314b7bbc61bd5d38237928694bdd">
bindings/python/.gitignore
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<li class="file-stats">
<a href="#533d8b0fbca07f6e97558d2396161599d8209742">
bindings/python/Makefile
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<li class="file-stats">
<a href="#7829dc991819ba4859fcdcd82bc1ea78ea57906e">
bindings/python/README.rst
→
bindings/python/README-tmpl.rst
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bindings/python/README.md
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<li class="file-stats">
<a href="#d803585b4b13aaa3cd9aa4aaf2fe7e5797750da5">
bindings/python/cedlib.pxd
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<a href="#0b5ebd1e73a970a851ab0b430b0efe417881144d">
bindings/python/edlib.pyx
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<a href="#2e7a0fef25a0e8843f022bc1badfb3500ec31fa3">
bindings/python/setup.py
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<a href="#b5e6d11fcc717483c4899727643243571563908e">
bindings/python/test.py
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#c5b12eedcbfaeb489795a3c470454f1eea540ffb">
debian/patches/cython3.patch
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<a href="#64b13b88ce64948b10e3d8c03b0badd31684a749">
debian/patches/enable_shared_and_static.patch
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<a href="#48e6df23def433866728dc58dedbaa6ffaddc0e4">
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debian/patches/really_exclude_readme.rst.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<span class="deleted-file">
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debian/patches/signed_char.patch
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debian/rules
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<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
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debian/salsa-ci.yml
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debian/upstream/metadata
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debian/watch
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edlib-config.cmake.in
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<a href="#250a624cf61d30af86e091990ce36ef46bcd0b59">
edlib.pc.in
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<a href="#1a7726f53bb6b76561c94b784c9e79695b9b074e">
edlib/include/edlib.h
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<a href="#99b7f95ca57c5f3e70bca1d739cd0f9cce7b542e">
edlib/src/edlib.cpp
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<span class="new-file">
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meson.build
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#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">@@ -24,3 +24,6 @@ callgrind.out.*</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">core</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">TAGS</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">/meson-build</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">/installation</span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># This ensures only commits on master, PRs towards master, and all tags are built.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Otherwise, build does not start.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">branch = master OR tag IS present</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># In order to catch as many weird edge cases in the code with -Werror as</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># possible, we want to test a large range of old and new compilers on both</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Linux and macOS. This gives us the best possible coverage while maintaining</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># compatibility with a large number of compilers.</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">stages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ccpp</span></span>
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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;">python</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">global</span><span class="pi">:</span></span>
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17
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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;">TWINE_USERNAME=Martinsos</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Encrypted TWINE_PASSWORD:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">secure</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">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"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"><span class="s" style="color: #d14;">.ccpp</span><span class="pi">:</span> <span class="nl">&ccpp</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">ccpp</span> <span class="c1" style="color: #998; font-style: italic;"># Builds C/CPP code.</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> </span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo -H pip3 install -U pip</span> <span class="c1" style="color: #998; font-style: italic;"># Needed for Meson.</span></span>
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26
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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;">sudo -H pip3 install -U setuptools</span> <span class="c1" style="color: #998; font-style: italic;"># Needed for Meson.</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${MATRIX_EVAL}"</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> </span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</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="s" style="color: #d14;">sudo -H pip3 install meson ninja</span> <span class="c1" style="color: #998; font-style: italic;"># We use Ninja both with Meson and CMake.</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> </span>
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build library and binaries using Meson and test them.</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Static library.</span></span>
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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;">make CXXFLAGS="-Werror" LIBRARY_TYPE=static BUILD_DIR=meson-build-static</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Shared library.</span></span>
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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;">make CXXFLAGS="-Werror" LIBRARY_TYPE=shared BUILD_DIR=meson-build-shared</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Check for memory leaks.</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># I run this only on linux because osx returns errors from</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># system libraries, which I would have to supress.</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="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="s" style="color: #d14;">make check-memory-leaks BUILD_DIR=meson-build-static</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build library and binaries with CMake and test them.</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -p build && cd build</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXXFLAGS="-Werror" cmake -GNinja ..</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ninja -v</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bin/runTests</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd ..</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"><span class="s" style="color: #d14;">.python</span><span class="pi">:</span> <span class="nl">&python</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span> <span class="c1" style="color: #998; font-style: italic;"># Builds python binding.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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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;">wget -qO- https://bootstrap.pypa.io/get-pip.py | python3</span></span>
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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;">python3 -m pip install cibuildwheel==1.6.1</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd bindings/python</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build the wheels, put them into './wheelhouse'.</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># cibuildwheel needs to be run from python directory.</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># The python directory is mounted in the docker build containers,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># so we need to copy the edlib source before running cibuild wheel.</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make edlib</span> <span class="c1" style="color: #998; font-style: italic;"># Copies edlib source to python dir.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="s" style="color: #d14;">CIBW_SKIP="cp27-* pp* *-manylinux_i686" \</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;">CIBW_BEFORE_BUILD="make sdist" \</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml"> <span class="s" style="color: #d14;">CIBW_TEST_COMMAND="python3 {project}/test.py" \</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m cibuildwheel --output-dir wheelhouse</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $DEPLOY_SDIST_TO_PYPI ]; then make sdist; fi</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Deploy wheel(s) and source (sdist) to PYPI (if commit is tagged).</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># NOTE: We are doing this in script section, and not in after_success,</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># because we want build to fail if deploying fails, which does not</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># happen if deployment is done inside after_success (that is how</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># travis works).</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># NOTE: We check TRAVIS_TEST_RESULT because we don't want to deploy</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># if building failed.</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ $TRAVIS_TEST_RESULT -eq 0 ]; then</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ $TRAVIS_TAG ]; then</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"> <span class="s" style="color: #d14;"># upgrade and upgrade-strategy-eager are here because of https://travis-ci.community/t/cant-deploy-to-pypi-anymore-pkg-resources-contextualversionconflict-importlib-metadata-0-18/10494/14 .</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m pip install --upgrade --upgrade-strategy eager twine</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload wheelhouse/*.whl</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml"> <span class="s" style="color: #d14;">if [ $DEPLOY_SDIST_TO_PYPI ]; then</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload dist/edlib-*.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="yaml"> <span class="s" style="color: #d14;">else</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="yaml"> <span class="s" style="color: #d14;">echo "Skipping twine upload because not a tag, files built:"</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -l wheelhouse</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -l dist</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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9
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GCC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># In order to catch as many weird edge cases in the code with -Werror as</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># possible, we want to test a large range of old and new compilers on both</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Linux and macOS. This gives us the best possible coverage while maintaining</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># compatibility with a large number of compilers.</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">C/CPP</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux;</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">GCC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4.9)"</span></span>
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11
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="yaml"> <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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12
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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13
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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14
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<td class="new_line diff-line-num old" data-linenumber="110" 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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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16
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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17
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.9</span></span>
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18
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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;">ninja-build</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">valgrind</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3-pip</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MATRIX_EVAL="export CC=gcc-4.9 && export CXX=g++-4.9"</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*ccpp</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">GCC</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">9</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">C/CPP</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux<span class="idiff">;</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">GCC</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">9</span>)"</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="yaml"> <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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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># For g++-9</span></span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-9</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ninja-build</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">valgrind</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3-pip</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MATRIX_EVAL="export CC=gcc-9 && export CXX=g++-9"</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*ccpp</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">5.0</span><span class="nv" style="color: #008080;"><span class="idiff left"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">(Linux</span>)"</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">C/CPP</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">(Linux;</span></span><span class="nv" style="color: #008080;"><span class="idiff right"> </span></span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">5.0)"</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="yaml"> <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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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-trusty-5.0</span></span>
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40
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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41
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-5.0</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;">ninja-build</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">valgrind</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python3-pip</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MATRIX_EVAL="export CC=clang-5.0 && export CXX=clang++-5.0"</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*ccpp</span></span>
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45
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">C<span class="idiff left">lang</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">X<span class="idiff">c</span>ode</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;"><span class="idiff">7.3</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">(Mac</span>)"</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">C<span class="idiff left">/CPP</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">(OSX;</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">X<span class="idiff">C</span>ode</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;"><span class="idiff">11;</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">Clang</span>)"</span></span>
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47
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="yaml"> <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="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode7.3</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">homebrew</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ninja</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">update</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode11</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*ccpp</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">wheel</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="yaml"> <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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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" 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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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># We need to upload sdist only once, since it is same for all jobs,</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># so with this flag we specify which job will take care of that (this one).</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">DEPLOY_SDIST_TO_PYPI="true"</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*python</span></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">Clang</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Xcode</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">11</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">(Mac</span>)"</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">Python</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">wheel</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">(OSX</span>)"</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="yaml"> <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="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode11</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">homebrew</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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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;">ninja</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># NOTE: Currently I commented out testing of python binding on OSX because they do not support</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Python building and I have to provide the tools myself. I could probably install correct pip</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># (and maybe python) version myself (homebrew?), however I haven't gotten to that yet.</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${MATRIX_EVAL}"</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then sudo apt-get install valgrind; fi</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then sudo -H pip install cython; fi</span> <span class="c1" style="color: #998; font-style: italic;"># Needed to build Python module.</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC74" 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="LC75" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build C/C++ library and apps.</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -p build && cd build && CXXFLAGS="-Werror" cmake -GNinja .. && ninja -v && cd ..</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build Python source distribution and install Edlib from it.</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then cd bindings/python && make sdist && cd ../..; fi</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then sudo -H pip install bindings/python/dist/edlib*.tar.gz; fi</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC82" 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="LC83" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Test C/C++ library using CTest.</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ninja -C build -v test && cat build/Testing/Temporary/LastTest.log</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Check for memory leaks. Returns 2 if there was a memory leak/error, otherwise returns runTests exit code,</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># which is 0 if all went fine or 1 if some of the tests failed. I test for memory leaks only on linux because</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># osx returns errors from system libraries, which I would have to supress.</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># This is run only on smaller number of tests, since executing on valgrind is slow.</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then valgrind --quiet --error-exitcode=2 --tool=memcheck --leak-check=full build/bin/runTests 2; fi</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Test Python module.</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == "linux" ]; then sudo -H python bindings/python/test.py; fi</span></span></pre>
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<pre style="margin: 0;">+<span id="LC166" 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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<pre style="margin: 0;">+<span id="LC167" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*python</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># TODO: Add windows x64 and linux aarch64 python wheel builds? Edlib users said they need them.</span></span></pre>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.2 FATAL_ERROR<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>edlib VERSION 1.2.5<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>edlib VERSION 1.2.6<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>EDLIB_ENABLE_INSTALL <span class="s2" style="color: #d14;">"Generate the install target"</span> ON<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>EDLIB_BUILD_EXAMPLES <span class="s2" style="color: #d14;">"Build examples"</span> ON<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>EDLIB_BUILD_UTILITIES <span class="s2" style="color: #d14;">"Build utilities"</span> ON<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">MACOSX</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SYSTEM_NAME</span><span class="si" style="color: #d14;">}</span> MATCHES <span class="s2" style="color: #d14;">"Darwin"</span><span class="p">))</span></span>
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5
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<td class="new_line diff-line-num" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"></span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +14,7 @@ endif()</td>
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10
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<td class="new_line diff-line-num" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>GNUInstallDirs<span class="p">)</span></span>
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11
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<td class="new_line diff-line-num" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CheckCXXCompilerFlag<span class="p">)</span></span>
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12
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<td class="new_line diff-line-num" 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="cmake"></span>
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13
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<td class="new_line diff-line-num old" data-linenumber="17" 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 1<span class="idiff left right">1</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 1<span class="idiff left right">4</span><span class="p">)</span></span>
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14
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<td class="new_line diff-line-num" data-linenumber="18" 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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD_REQUIRED ON<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Falling back to different standard it not allowed.</span></span>
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15
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<td class="new_line diff-line-num" 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">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_EXTENSIONS OFF<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Make sure no compiler-specific features are used.</span></span>
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16
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cmake"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" 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="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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,18 +52,29 @@ file(GLOB SOURCES "edlib/src/*.cpp")</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cmake"></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Create libraries.</span></span>
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50
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>edlib <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SOURCES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>edlib::edlib ALIAS edlib<span class="p">)</span></span>
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51
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span>edlib</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cmake"> PROPERTIES</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> PROPERTIES</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> CXX_VISIBILITY_PRESET hidden</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"> VISIBILITY_INLINES_HIDDEN ON</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cmake"> VERSION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_VERSION</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cmake"> SOVERSION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_VERSION</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"> SOVERSION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_VERSION_MAJOR</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>edlib PRIVATE DLIB_BUILD<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>BUILD_SHARED_LIBS<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>edlib PUBLIC EDLIB_SHARED<span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_include_directories</span><span class="p">(</span>edlib PUBLIC</span>
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57
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/edlib/include></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cmake"> $<INSTALL_INTERFACE:<span class="idiff left right">include</span>><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cmake"> $<INSTALL_INTERFACE:<span class="si" style="color: #d14;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">CMAKE_INSTALL_INCLUDEDIR</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span>><span class="p">)</span></span>
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59
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Build binaries.</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>helloWorld apps/hello-world/helloWorld.c<span class="p">)</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>helloWorld edlib<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>EDLIB_BUILD_EXAMPLES<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>helloWorld apps/hello-world/helloWorld.c<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>helloWorld edlib<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CTest<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_TESTING<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" 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">@@ -69,19 +84,63 @@ if (BUILD_TESTING)</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_test</span><span class="p">(</span>edlib_tests <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_RUNTIME_OUTPUT_DIRECTORY</span><span class="si" style="color: #d14;">}</span>/runTests<span class="p">)</span></span>
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70
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT WIN32<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># If on windows, do not build binaries that do not support windows.</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>edlib-aligner apps/aligner/aligner.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>edlib-aligner edlib<span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>EDLIB_BUILD_UTILITIES<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT WIN32<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># If on windows, do not build binaries that do not support windows.</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>edlib-aligner apps/aligner/aligner.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>edlib-aligner edlib<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Create target 'install' for installing libraries.</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS edlib DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>FILES edlib/include/edlib.h DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_INCLUDEDIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cmake"></span>
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82
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># configure and install pkg-config file</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PKG_EDLIB_DEFS <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">get_target_property</span><span class="p">(</span>EDLIB_INTERFACE_DEFS edlib INTERFACE_COMPILE_DEFINITIONS<span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">NOT</span> <span class="p">(</span>EDLIB_INTERFACE_DEFS STREQUAL <span class="s2" style="color: #d14;">"NOTFOUND"</span> OR EDLIB_INTERFACE_DEFS STREQUAL <span class="s2" style="color: #d14;">"EDLIB_INTERFACE_DEFS-NOTFOUND"</span><span class="p">))</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">foreach</span><span class="p">(</span>EDLIB_INTERFACE_DEF <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">EDLIB_INTERFACE_DEFS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND PKG_EDLIB_DEFS <span class="s2" style="color: #d14;">"-D</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">EDLIB_INTERFACE_DEF</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endforeach</span><span class="p">()</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">string</span><span class="p">(</span>REPLACE <span class="s2" style="color: #d14;">";"</span> <span class="s2" style="color: #d14;">" "</span> PKG_EDLIB_DEFS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PKG_EDLIB_DEFS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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83
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">configure_file</span><span class="p">(</span></span>
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84
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/edlib.pc.in</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/edlib-<span class="idiff left right">1</span>.pc</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/edlib-<span class="si" style="color: #d14;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">PROJECT_VERSION_MAJOR</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span>.pc</span>
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86
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cmake"> @ONLY<span class="p">)</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>FILES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/edlib-1.pc DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span>/pkgconfig<span class="p">)</span></span></pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cmake"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>EDLIB_ENABLE_INSTALL<span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>FILES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/edlib-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_VERSION_MAJOR</span><span class="si" style="color: #d14;">}</span>.pc DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span>/pkgconfig<span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CMakePackageConfigHelpers<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>EDLIB_CMAKE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/cmake/edlib"</span> CACHE STRING</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"Installation directory for cmake files, relative to </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_PREFIX</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">."</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>version_config <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/edlib-config-version.cmake"</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>project_config <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/edlib-config.cmake"</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>targets_export_name edlib-targets<span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cmake"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># Generate the version, config and target files into the build directory.</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">write_basic_package_version_file</span><span class="p">(</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">version_config</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cmake"> VERSION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="si" style="color: #d14;">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cmake"> COMPATIBILITY AnyNewerVersion<span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">configure_package_config_file</span><span class="p">(</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/edlib-config.cmake.in</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">project_config</span><span class="si" style="color: #d14;">}</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cmake"> INSTALL_DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">EDLIB_CMAKE_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">export</span><span class="p">(</span>TARGETS edlib NAMESPACE edlib::</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cmake"> FILE <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">targets_export_name</span><span class="si" style="color: #d14;">}</span>.cmake<span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cmake"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># Install version, config and target files.</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># These are cmake config files and they are useful for some consumers, for example vcpkg.</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cmake"> FILES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">project_config</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">version_config</span><span class="si" style="color: #d14;">}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">EDLIB_CMAKE_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>EXPORT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">targets_export_name</span><span class="si" style="color: #d14;">}</span> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">EDLIB_CMAKE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cmake"> NAMESPACE edlib::<span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cmake"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># Create target 'install' for installing libraries.</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cmake"> TARGETS edlib</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cmake"> EXPORT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">targets_export_name</span><span class="si" style="color: #d14;">}</span> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cmake"> RUNTIME DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_BINDIR</span><span class="si" style="color: #d14;">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cmake"> LIBRARY DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cmake"> ARCHIVE DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>FILES edlib/include/edlib.h DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_INCLUDEDIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">BUILD_DIR</span> <span class="o" style="font-weight: 600;">?=</span> meson-build</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Can be 'static' or 'shared'.</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">LIBRARY_TYPE</span> <span class="o" style="font-weight: 600;">?=</span> static</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">TEST_DATA_DIR</span> <span class="o" style="font-weight: 600;">?=</span> apps/aligner/test_data</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">YELLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\0</span>33[33m</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">GREEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\0</span>33[32m</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">BOLD</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\0</span>33[1m</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">RESET</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\0</span>33[0m</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">${YELLOW}${BOLD}</span><span class="s2" style="color: #d14;">Configuring build setup via Meson...</span><span class="nv" style="color: #008080;">${RESET}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"> <span class="nv" style="color: #008080;">${MAKE}</span> configure</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="nv" style="color: #008080;">${YELLOW}${BOLD}</span><span class="s2" style="color: #d14;">Building </span><span class="nv" style="color: #008080;">${LIBRARY_TYPE}</span><span class="s2" style="color: #d14;"> library and binaries...</span><span class="nv" style="color: #008080;">${RESET}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"> <span class="nv" style="color: #008080;">${MAKE}</span> build</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="nv" style="color: #008080;">${YELLOW}${BOLD}</span><span class="s2" style="color: #d14;">Running tests...</span><span class="nv" style="color: #008080;">${RESET}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"> <span class="nv" style="color: #008080;">${MAKE}</span> <span class="nb" style="color: #0086b3;">test</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="nv" style="color: #008080;">${GREEN}${BOLD}</span><span class="s2" style="color: #d14;">Edlib successfully built! You can find built binaries and libraries in </span><span class="nv" style="color: #008080;">${BUILD_DIR}</span><span class="s2" style="color: #d14;">/ directory.</span><span class="nv" style="color: #008080;">${RESET}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nl">configure</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">${BUILD_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"> meson setup <span class="nv" style="color: #008080;">${BUILD_DIR}</span> <span class="nb" style="color: #0086b3;">.</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> <span class="nt" style="color: #000080;">--backend</span><span class="o" style="font-weight: 600;">=</span>ninja <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"> <span class="nt" style="color: #000080;">-Ddefault_library</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">${LIBRARY_TYPE}</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nl">build</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"> meson compile <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">${BUILD_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"> meson <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">${BUILD_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Valgrind Returns 2 if there was a memory leak/error,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># otherwise returns runTests exit code, which is 0 if</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># all went fine or 1 if some of the tests failed.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make"><span class="nl">check-memory-leaks</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> valgrind <span class="nv" style="color: #008080;">${BUILD_DIR}</span>/runTests 2 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"> <span class="nt" style="color: #000080;">--quiet</span> <span class="nt" style="color: #000080;">--error-exitcode</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nt" style="color: #000080;">--tool</span><span class="o" style="font-weight: 600;">=</span>memcheck <span class="nt" style="color: #000080;">--leak-check</span><span class="o" style="font-weight: 600;">=</span>full</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> meson <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">${BUILD_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">${BUILD_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all build configure test install clean check-memory-leaks</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown">Edlib</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="ni" style="color: #800080;">·</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Latest Github release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/Martinsos/edlib.svg</span><span class="p">)</span>](https://github.com/Martinsos/edlib/releases/latest)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status of the master branch on Linux/OSX</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/travis/Martinsos/edlib/master<span class="idiff left">.svg</span>?label=Linux%20%2F%20OSX%20build</span><span class="p">)</span>](https://travis-ci.<span class="idiff right">org</span>/Martinsos/edlib)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status of the master branch on Windows</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/appveyor/<span class="idiff left">ci</span>/Martinsos/edlib<span class="idiff right">.svg</span>?label=Windows%20build</span><span class="p">)</span>](https://ci.appveyor.com/project/Martinsos/edlib/branch/master)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status of the master branch on Linux/OSX</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/travis/Martinsos/edlib/master?label=Linux%20%2F%20OSX%20build</span><span class="p">)</span>](https://travis-ci.<span class="idiff left right">com</span>/Martinsos/edlib)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status of the master branch on Windows</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/appveyor/<span class="idiff left">build</span>/Martinsos/edlib<span class="idiff right">/master</span>?label=Windows%20build</span><span class="p">)</span>](https://ci.appveyor.com/project/Martinsos/edlib/branch/master)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Chat on Gitter</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/gitter/room/Martinsos/edlib.svg?colorB=753a88</span><span class="p">)</span>](https://gitter.im/Martinsos/edlib)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">[](https://doi.org/10.1093/bioinformatics/btw753)</span></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;">=====</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -14,6 +14,10 @@ Calculating edit distance of two strings is as simple as:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="n" style="color: #333;">edlibAlign</span><span class="p">(</span><span class="s" style="color: #d14;">"hello"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="s" style="color: #d14;">"world!"</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">edlibDefaultAlignConfig</span><span class="p">()).</span><span class="n" style="color: #333;">editDistance</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">Edlib is also available for <span class="gs" style="font-weight: 600;">**Python**</span> <span class="p">[</span><span class="nv" style="color: #008080;">![PyPI version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/pypi/v/edlib.svg</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Click</span> here for Python README)](https://pypi.python.org/pypi/edlib), with code residing at <span class="p">[</span><span class="nv" style="color: #008080;">bindings/python</span><span class="p">](</span><span class="sx" style="color: #d14;">bindings/python</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">There is also non-official <span class="p">[</span><span class="nv" style="color: #008080;">binding for Julia</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/cjdoris/Edlib.jl</span><span class="p">)</span> by @cjdoris.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Features</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">*</span> Calculates <span class="gs" style="font-weight: 600;">**edit distance (Levenshtein distance)**</span>.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">*</span> It can find <span class="gs" style="font-weight: 600;">**optimal alignment path**</span> (instructions how to transform first sequence into the second sequence).</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">@@ -23,8 +27,6 @@ edlibAlign("hello", 5, "world!", 6, edlibDefaultAlignConfig()).editDistance;</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="p">*</span> It can easily handle small or <span class="gs" style="font-weight: 600;">**very large sequences**</span>, even when finding alignment path, while consuming very little memory.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="p">*</span> <span class="gs" style="font-weight: 600;">**Super fast**</span> thanks to Myers's bit-vector algorithm.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">Edlib is also available for <span class="gs" style="font-weight: 600;">**Python**</span> <span class="p">[</span><span class="nv" style="color: #008080;">![PyPI version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/pypi/v/edlib.svg</span><span class="p">)</span>](https://pypi.python.org/pypi/edlib) and <span class="gs" style="font-weight: 600;">**Node.js**</span> <span class="p">[</span><span class="nv" style="color: #008080;">![npm version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/npm/v/node-edlib.svg</span><span class="p">)</span>](https://www.npmjs.com/package/node-edlib).</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Features</span><span class="p">](</span><span class="sx" style="color: #d14;">#features</span><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">@@ -42,22 +44,6 @@ Edlib is also available for **Python** [![PyPI version](https://img.shields.io/p</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Acknowledgements</span><span class="p">](</span><span class="sx" style="color: #d14;">#acknowledgements</span><span class="p">)</span></span>
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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>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Building</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown">Edlib uses CMAKE to build libraries (static and shared) and binaries (apps and tests).</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown">Execute following commands to build Edlib using CMAKE:</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="p">1.</span> <span class="sb" style="color: #d14;">`cd build`</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="p">2.</span> <span class="sb" style="color: #d14;">`cmake -D CMAKE_BUILD_TYPE=Release ..`</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="p">3.</span> <span class="sb" style="color: #d14;">`make`</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown">This will create binaries in <span class="sb" style="color: #d14;">`bin/`</span> directory and libraries (static and shared) in <span class="sb" style="color: #d14;">`lib/`</span> directory.</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown">You can run <span class="sb" style="color: #d14;">`./bin/runTests`</span> to confirm that it works!</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown">Optionally, you can run <span class="sb" style="color: #d14;">`sudo make install`</span> to install edlib library on your machine (on Linux, this will usually install it to <span class="sb" style="color: #d14;">`usr/local/lib`</span> and <span class="sb" style="color: #d14;">`usr/local/include`</span>).</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">You may also install edlib using Conda <span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda-Server Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/edlib/badges/installer/conda.svg</span><span class="p">)</span>](https://conda.anaconda.org/bioconda): <span class="sb" style="color: #d14;">`conda install edlib`</span>.</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Using Edlib in your project</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown">You can use Edlib in you project by either directly copying header and source files from <span class="p">[</span><span class="nv" style="color: #008080;">edlib/</span><span class="p">](</span><span class="sx" style="color: #d14;">edlib/</span><span class="p">)</span>, or by linking Edlib library (see <span class="p">[</span><span class="nv" style="color: #008080;">Building</span><span class="p">](</span><span class="sx" style="color: #d14;">#building</span><span class="p">)</span> for instructions how to build Edlib libraries).</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown">In any case, only thing that you have to do in your source files is to include <span class="sb" style="color: #d14;">`edlib.h`</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">@@ -113,10 +99,11 @@ helloWorld.cpp -> your program</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown">Now you can compile it with <span class="sb" style="color: #d14;">`c++ helloWorld.cpp -o helloWorld -I edlib/include -L edlib -ledlib`</span>.</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Approach #3: Install edlib library on machine.</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown">Alternatively, you could avoid copying any Edlib files and instead install libraries by running <span class="sb" style="color: #d14;">`sudo make install`</span> (check <span class="p">[</span><span class="nv" style="color: #008080;">Building</span><span class="p">](</span><span class="sx" style="color: #d14;">#building</span><span class="p">)</span>). Now, all you have to do to compile your project is <span class="sb" style="color: #d14;">`c++ helloWorld.cpp -o helloWorld -ledlib`</span>.</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">Alternatively, you could avoid copying any Edlib files and instead install libraries by running <span class="sb" style="color: #d14;">`sudo make install`</span> (check <span class="p">[</span><span class="nv" style="color: #008080;">Building</span><span class="p">](</span><span class="sx" style="color: #d14;">#building</span><span class="p">)</span><span class="idiff left right"> for exact instructions depending on approach you used for building</span>). Now, all you have to do to compile your project is <span class="sb" style="color: #d14;">`c++ helloWorld.cpp -o helloWorld -ledlib`</span>.</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown">If you get error message like <span class="sb" style="color: #d14;">`cannot open shared object file: No such file or directory`</span>, make sure that your linker includes path where edlib was installed.</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Approach #4: Use edlib in your project via CMake.</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Using git submodule</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown">If you are using CMake for compilation, we suggest adding edlib as a git submodule with the command <span class="sb" style="color: #d14;">`git submodule add https://github.com/martinsos/edlib vendor/edlib`</span>. Afterwards, modify your top level CMakeLists.txt file accordingly:</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown">add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)</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">@@ -127,6 +114,65 @@ The `add_subdirectory` command adds a folder to the build tree, meaning it will</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown">For more example projects take a look at applications in <span class="p">[</span><span class="nv" style="color: #008080;">apps/</span><span class="p">](</span><span class="sx" style="color: #d14;">apps/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Using VCPKG</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown">Edlib is available on <span class="p">[</span><span class="nv" style="color: #008080;">VCPKG</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/microsoft/vcpkg</span><span class="p">)</span> package manager. With VCPKG on your system, Edlib can be downloaded using the VCPKG install command <span class="sb" style="color: #d14;">`vcpkg install edlib`</span>. Once the library has been downloaded, add the following instructions to your CMakeLists.txt file:</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown">find_package(edlib CONFIG REQUIRED)</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown">target_link_libraries(MyProject PRIVATE edlib::edlib)</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown">then you should be able to include the library header in your project (<span class="sb" style="color: #d14;">`#include "edlib.h`</span>)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Building</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Meson</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown">Primary way of building Edlib is via <span class="p">[</span><span class="nv" style="color: #008080;">Meson</span><span class="p">](</span><span class="sx" style="color: #d14;">https://mesonbuild.com/</span><span class="p">)</span> build tool.</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown">Requirements: make sure that you have <span class="sb" style="color: #d14;">`meson`</span> installed on your system.</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown">Execute</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown">to build <span class="gs" style="font-weight: 600;">**static**</span> library and binaries (apps and tests) and also run tests. </span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown">To build <span class="gs" style="font-weight: 600;">**shared**</span> library and binaries, do <span class="sb" style="color: #d14;">`make LIBRARY_TYPE=shared`</span>.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">Library and binaries will be created in <span class="sb" style="color: #d14;">`meson-build`</span> directory. </span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown">You can choose alternate build directory like this: <span class="sb" style="color: #d14;">`make BUILD_DIR=some-other-dir`</span>.</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown">Optionally, you can run</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown">sudo make install</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown">to install edlib library on your machine (on Linux, this will usually install it to <span class="sb" style="color: #d14;">`usr/local/lib`</span> and <span class="sb" style="color: #d14;">`usr/local/include`</span>).</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown">Check Makefile if you want to run individual steps on your own (building, tests, ...).</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown">NOTE: If you need more control, use <span class="sb" style="color: #d14;">`meson`</span> command directly, <span class="sb" style="color: #d14;">`Makefile`</span> is here only to help with common commands.</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### CMake</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown">Edlib can alternatively be built with CMake.</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown">Execute following command to build Edlib using CMAKE:</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="p">```</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown">cd build && cmake -D CMAKE_BUILD_TYPE=Release .. && make</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown">This will create binaries in <span class="sb" style="color: #d14;">`bin/`</span> directory and libraries (static and shared) in <span class="sb" style="color: #d14;">`lib/`</span> directory.</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown">./bin/runTests</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="p">```</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown">to run tests.</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown">Optionally, you can run</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown">sudo make install</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown">to install edlib library on your machine.</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Conda</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown">Edlib can also be installed via Conda: <span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda-Server Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/edlib/badges/installer/conda.svg</span><span class="p">)</span>](https://conda.anaconda.org/bioconda): <span class="sb" style="color: #d14;">`conda install edlib`</span>.</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"></span>
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130
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="markdown"></span>
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131
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage and examples</span></span>
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132
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="markdown">Main function in edlib is <span class="sb" style="color: #d14;">`edlibAlign`</span>. Given two sequences (and their lengths), it will find edit distance, alignment path or its end and start locations.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" 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="309" 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">@@ -263,3 +309,8 @@ Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequenc</td>
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263
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown">Mile Šikić (@msikic) - Mentoring and guidance through whole project.</span>
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264
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown"></span>
</pre>
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265
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="markdown">Ivan Sović (@isovic) - Help with testing and prioritizing features, valuable comments on the manuscript.</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="266" 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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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## FAQ</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="315" 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="LC315" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### What do terms NW, HW and SHW stand for?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" 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="LC316" class="line" lang="markdown">NW stands for Needleman-Wunsch, HW for Hybrid Wunsch, and SHW for Semi Hybrid Wunsch. While NW is a common abbreviation, HW and SHW abbreviations were made up at the very start of this project to describe additional modes of alignment. Later we started using terms "global", "infix" and "prefix" more, as they describe the modes better, but terms NW, HW and SHW are still very present in the project.</span></pre>
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<br>
</li>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#43b9d80d1f50472e56afb94a061257af5b53182b"><strong>appveyor.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">platform</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">x64</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">x86</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">x64</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">environment</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span> <span class="c1" style="color: #998; font-style: italic;"># This will still build PRs.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># VS 2010</span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;"><span class="idiff left">BUILD_TYPE</span></span><span class="pi"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">cmake</span></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="idiff left"> </span><span class="na" style="color: #008080;"><span class="idiff">VS_VERSION</span></span><span class="pi"><span class="idiff">:</span></span> <span class="s" style="color: #d14;">Visual Studio </span><span class="m" style="color: #099;"><span class="idiff right">10</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;"><span class="idiff left">image</span></span><span class="pi"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left">Visual Studio </span></span><span class="m" style="color: #099;"><span class="idiff right">2017</span></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi"><span class="idiff left">-</span></span> <span class="s" style="color: #d14;">Visual Studio </span><span class="m" style="color: #099;"><span class="idiff right">2019</span></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># VS 2012</span></span>
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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;">BUILD_TYPE</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">VS_VERSION</span><span class="pi">:</span> <span class="s" style="color: #d14;">Visual Studio </span><span class="m" style="color: #099;">11</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">environment</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">x86</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">x64</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># VS 2013</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">BUILD_TYPE</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">VS_VERSION</span><span class="pi">:</span> <span class="s" style="color: #d14;">Visual Studio </span><span class="m" style="color: #099;">12</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Configuration for Meson</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if %arch%==x86 (set PYTHON_ROOT=C:\python37) else (set PYTHON_ROOT=C:\python37-x64)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">echo Using Python at %PYTHON_ROOT%</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">set PATH=%cd%;%PYTHON_ROOT%;%PYTHON_ROOT%\Scripts;%PATH%</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">pip install ninja meson</span></span>
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19
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">shallow_clone</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Enable using MSVC through command line.</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%APPVEYOR_BUILD_WORKER_IMAGE%"=="Visual Studio 2017" ( call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" %arch% )</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%APPVEYOR_BUILD_WORKER_IMAGE%"=="Visual Studio 2019" ( call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat" %arch% )</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;">build_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if "%platform%" == "x64" SET VS_FULL=%VS_VERSION% Win64</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if "%platform%" == "x86" SET VS_FULL=%VS_VERSION%</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -G "%VS_FULL%" .</span></span>
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26
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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;">cmake --build . --config Release</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">echo Building on image %APPVEYOR_BUILD_WORKER_IMAGE%, arch %arch%.</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build with CMake (builds both static and shared library).</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%APPVEYOR_BUILD_WORKER_IMAGE%"=="Visual Studio 2017" ( SET "GENERATOR_VS_VERSION=Visual Studio 15 2017" )</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%APPVEYOR_BUILD_WORKER_IMAGE%"=="Visual Studio 2019" ( SET "GENERATOR_VS_VERSION=Visual Studio 16 2019" )</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%arch%"=="x86" ( SET "GENERATOR_VS_ARCH=Win32" )</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">if "%arch%"=="x64" ( SET "GENERATOR_VS_ARCH=x64" )</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake -G "%GENERATOR_VS_VERSION%" -A %GENERATOR_VS_ARCH% .</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake --build . --config Release</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build with Meson.</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Static library.</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson setup --backend=ninja -Ddefault_library=static meson-build-static .</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson compile -v -C meson-build-static</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Shared library.</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="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson setup --backend=ninja -Ddefault_library=shared meson-build-shared .</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson compile -v -C meson-build-shared</span></span>
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27
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"><span class="na" style="color: #008080;">test_script</span><span class="pi">:</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bin\Release\runTests.exe</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Test what CMake built.</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">bin\Release\runTests.exe</span></span>
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30
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"><span class="na" style="color: #008080;">deploy</span><span class="pi">:</span> <span class="s" style="color: #d14;">off</span></span></pre>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Test what Meson built.</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson test -C meson-build-static</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">cmd</span><span class="pi">:</span> <span class="s" style="color: #d14;">meson test -C meson-build-shared</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#afbead18ab75314b7bbc61bd5d38237928694bdd"><strong>bindings/python/.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">@@ -6,3 +6,5 @@ edlib.c</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">edlib.*.so</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.eggs/</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">*.bycython.*</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">README.rst</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">README.html</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#533d8b0fbca07f6e97558d2396161599d8209742"><strong>bindings/python/Makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nl">default</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">build</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">############### FILES #################</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">FILES</span><span class="o" style="font-weight: 600;">=</span>edlib pyedlib.bycython.cpp setup.py MANIFEST.in README.rst</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="nl">edlib</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">../../edlib</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-R</span> ../../edlib .</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="nl">edlib</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(shell find ../../edlib)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># create a clean </span><span class="o" style="font-weight: 600;">(</span>maybe updated<span class="o" style="font-weight: 600;">)</span> copy of edlib src</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> edlib <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> ../../edlib .</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nl">pyedlib.bycython.cpp</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">edlib.pyx cedlib.pxd</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"> python <span class="nt" style="color: #000080;">-m</span> pip <span class="nb" style="color: #0086b3;">install </span>cython</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"> cython <span class="nt" style="color: #000080;">--cplus</span> edlib.pyx <span class="nt" style="color: #000080;">-o</span> edlib.bycython.cpp</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#######################################</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">############## COMMANDS ###############</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"><span class="nl">build</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${FILES}</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># To build package, README.rst is needed, because it goes into long description of package,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># which is what is visible on PyPI.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># However, to generate README.rst from README-tmpl.rst, built package is needed (for `import edlib` in cog)!</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Therefore, we first build package without README.rst, use it to generate README.rst,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># and then finally build package again but with README.rst.</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="nv" style="color: #008080;">BUILD_SOURCE_FILES</span><span class="o" style="font-weight: 600;">=</span>edlib pyedlib.bycython.cpp setup.py</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nl">buildWithoutREADME.rst</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${BUILD_SOURCE_FILES}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"> <span class="nv" style="color: #008080;">EDLIB_OMIT_README_RST</span><span class="o" style="font-weight: 600;">=</span>1 python setup.py build_ext <span class="nt" style="color: #000080;">-i</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="nl">README.rst</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">buildWithoutREADME.rst README-tmpl.rst</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"> python <span class="nt" style="color: #000080;">-m</span> pip <span class="nb" style="color: #0086b3;">install </span>cogapp</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> cog <span class="nt" style="color: #000080;">-d</span> <span class="nt" style="color: #000080;">-o</span> README.rst README-tmpl.rst </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="nv" style="color: #008080;">BUILD_FILES</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">${BUILD_SOURCE_FILES}</span> README.rst</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="nl">build</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${BUILD_FILES}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> python setup.py build_ext <span class="nt" style="color: #000080;">-i</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="nl">sdist</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">${FILES}</span></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"><span class="nl">sdist</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">edlib pyedlib.bycython.cpp setup.py README.rst MANIFEST.in</span></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"> python setup.py sdist</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">publish</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean sdist</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">@@ -23,4 +38,4 @@ publish: clean sdist</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> edlib dist edlib.egg-info build</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> edlib.c <span class="k" style="font-weight: 600;">*</span>.bycython.<span class="k" style="font-weight: 600;">*</span> edlib.<span class="k" style="font-weight: 600;">*</span>.so</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#######################################</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff right"> README.rst</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#7829dc991819ba4859fcdcd82bc1ea78ea57906e"><strong>bindings/python/README.rst</strong>
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<strong>bindings/python/README-tmpl.rst</strong>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. [[[cog</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> import cog</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> import edlib</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> def indent(text, indentation = " "):</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> return indentation + text.replace("\n", "\n" + indentation)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> def comment(text):</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> return "# " + text.replace("\n", "\n# ")</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> def cogOutExpression(expr):</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> cog.outl(indent(expr))</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> cog.outl(indent(comment(str(eval(expr)))))</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ]]]</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> [[[end]]]</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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1
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">=====</span>
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2
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Edlib</span>
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3
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">=====</span>
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4
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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5
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.</span>
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6
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.. code:: python</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> edlib.align("hello", "world")</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Popular use cases: aligning DNA sequences, calculating word/text similarity.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.. [[[cog</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> </span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> cog.outl()</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> cog.outl(".. code:: python")</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> cog.outl()</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> </span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> cogOutExpression('edlib.align("elephant", "telephone")')</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> cog.outl()</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> </span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> cog.outl(indent(comment('Works with unicode characters (or any other iterable of hashable objects)!')))</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> cogOutExpression('edlib.align("ты милая", "ты гений")')</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> cog.outl()</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> cogOutExpression('edlib.align("AACG", "TCAACCTG", mode = "HW", task = "path")')</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> cog.outl()</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> cog.outl(indent('query = "elephant"; target = "telephone"'))</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> cog.outl(indent(comment('NOTE: `task` has to be "path" in order to get nice alignment.')))</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> cog.outl(indent('result = edlib.align(query, target, task = "path")'))</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> cog.outl(indent('nice = edlib.getNiceAlignment(result, query, target)'))</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> cog.outl(indent('print("\\n".join(nice.values()))'))</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> query = "elephant"; target = "telephone"</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> result = edlib.align(query, target, task = "path")</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> nice = edlib.getNiceAlignment(result, query, target)</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> output = "\n".join(nice.values())</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> cog.outl(indent(comment(output)))</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> cog.outl()</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> ]]]</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.. code::</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> {{ Basic code examples will be generated here. }}</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.. [[[end]]]</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">Edlib is actually a C/C++ library, and this package is it's wrapper for Python.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Python Edlib has mostly the same API as C/C++ Edlib, so <span class="idiff left right">make sur</span>e to check out `C/C++ Edlib docs <http://github.com/Martinsos/edlib>`_ for more code examples, details on API and how Edlib works.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Python Edlib has mostly the same API as C/C++ Edlib, so <span class="idiff left right">feel fre</span>e to check out `C/C++ Edlib docs <http://github.com/Martinsos/edlib>`_ for more code examples, details on API and how Edlib works.</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">--------</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">Features</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">@@ -23,7 +76,7 @@ Features</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">* It can easily handle small or **very large** sequences, even when finding alignment path.</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">* **Super fast** thanks to Myers's bit-vector algorithm.</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">NOTE<span class="idiff left right">: Size of alphabet</span> has to be <= 256 (meaning that query and target together must have <= 256 unique values).</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"><span class="idiff left">**</span>NOTE<span class="idiff">**: **Alphabet length</span> has to be <= 256<span class="idiff right">**</span> (meaning that query and target together must have <= 256 unique values).</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">------------</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">Installation</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">@@ -36,47 +89,97 @@ Installation</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">API</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Edlib has two functions, `align()` and `getNiceAlignment()`:</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Edlib has two functions, ``align()`` and ``getNiceAlignment()``:</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">align()</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> align(query, target, [mode], [task], [k])</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> align(query, target, [mode], [task], [k], [additionalEqualities])</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Aligns ``query`` against ``target`` with edit distance.</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">``query`` and ``target`` can be strings, bytes, or any iterables of hashable objects, as long as all together they don't have more than 256 unique values.</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.. [[[cog</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> import pydoc</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> help_str = pydoc.plain(pydoc.render_doc(edlib.align, "%s"))</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> cog.outl()</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> cog.outl('Output of ``help(edlib.align)``:')</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> cog.outl()</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> cog.outl('.. code::\n')</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> cog.outl(indent(help_str))</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> ]]]</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.. code::</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> {{ Content of help(edlib.align) will be generated here. }}</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.. [[[end]]]</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">getNiceAlignment()</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">------------------</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> getNiceAlignment(alignResutl, query, target)</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> getNiceAlignment(alignResult, query, target)</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Represents alignment from ``align()`` in a visually attractive format.</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.. [[[cog</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> import pydoc</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> help_str = pydoc.plain(pydoc.render_doc(edlib.getNiceAlignment, "%s"))</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> cog.outl()</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> cog.outl('Output of ``help(edlib.getNiceAlignment)``:')</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> cog.outl()</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> cog.outl('.. code::\n')</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> cog.outl(indent(help_str))</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> ]]]</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.. code::</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> {{ Content of help(edlib.getNiceAlignment) will be generated here. }}</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.. [[[end]]]</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">To learn more about it, type :code:`help(edlib.align)` in your python interpreter.</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext">-----</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">-----</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> import edlib</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">.. [[[cog</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> cog.outl()</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> cog.outl(".. code:: python")</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> cog.outl()</span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> result = edlib.align("elephant", "telephone")</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> print(result["editDistance"]) # 3</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> print(result["alphabetLength"]) # 8</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> print(result["locations"]) # [(None, 8)]</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> print(result["cigar"]) # None</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> cog.outl(indent('import edlib'))</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> cog.outl()</span>
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65
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> result = edlib.align("ACTG", "CACTRT", mode="HW", task="path", additionalEqualities=[("R", "A"), ("R", "G")])</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> print(result["editDistance"]) # 0</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> print(result["alphabetLength"]) # 5</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> print(result["locations"]) # [(1, 4)]</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> print(result["cigar"]) # "4="</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> cogOutExpression('edlib.align("ACTG", "CACTRT", mode="HW", task="path")')</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> cog.outl()</span>
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71
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> result = edlib.align("elephant", "telephone", task="path") ## users must use 'task="path"' </span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> niceAlign = edlib.getNiceAlignment(result, "elephant", "telephone")</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> print(niceAlign['query_aligned']) # "-elephant"</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> print(niceAlign['matched_aligned']) # "-|||||.|."</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> print(niceAlign['target_aligned']) # "telephone"</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> cog.outl(indent(comment('You can provide additional equalities.')))</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> cogOutExpression('edlib.align("ACTG", "CACTRT", mode="HW", task="path", additionalEqualities=[("R", "A"), ("R", "G")])')</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> cog.outl()</span>
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77
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> ]]]</span>
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78
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.. code::</span>
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79
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> {{ Additional usage examples will be generated here. }}</span>
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180
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">.. [[[end]]]</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">Benchmark</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">@@ -123,12 +226,5 @@ Check out `C/C++ Edlib docs <http://github.com/Martinsos/edlib>`_ for more infor</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext">Development</span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">-----------</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">Run :code:`make build` to generate an extension module as .so file. You can test it then by importing it from python interpreter :code:`import edlib` and running :code:`edlib.align(...)` (you have to be positioned in the directory where .so was built). This is useful for testing while developing.</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">Run :code:`make sdist` to create a source distribution, but not publish it - it is a tarball in dist/ that will be uploaded to pip on `publish`. Use this to check that tarball is well structured and contains all needed files, before you publish.</span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">Good way to test it is to run :code:`sudo pip install dist/edlib-*.tar.gz`, which will try to install edlib from it, same way as pip will do it when it is published.</span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">Run :code:`make publish` to create a source distribution and publish it to the PyPI. Use this to publish new version of package.</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">Make sure to bump the version in `setup.py` before publishing, if needed.</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">Check out `Edlib python package on Github <https://github.com/Martinsos/edlib/tree/master/bindings/python>`_.</span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">:code:`make clean` removes all generated files.</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#2fd9ec2790c10a208e05eccc8896733d5040b2eb"><strong>bindings/python/README.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Edlib python package</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">This README contains only development information, you can check out full README (README.rst) for the latest version of Edlib python package on <span class="p">[</span><span class="nv" style="color: #008080;">Edlib's PyPI page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pypi.org/project/edlib/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">README.rst is not commited to git because it is generated from <span class="p">[</span><span class="nv" style="color: #008080;">README-tmpl.rst</span><span class="p">](</span><span class="sx" style="color: #d14;">./README-tmpl.rst</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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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;">## Building</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">Run <span class="sb" style="color: #d14;">`make build`</span> to generate an extension module as .so file.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">You can test it then by importing it from python interpreter <span class="sb" style="color: #d14;">`import edlib`</span> and running <span class="sb" style="color: #d14;">`edlib.align(...)`</span> (you have to be positioned in the directory where .so was built).</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">This is useful for testing while developing.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">Run <span class="sb" style="color: #d14;">`make sdist`</span> to create a source distribution, but not publish it - it is a tarball in dist/ that will be uploaded to pip on <span class="sb" style="color: #d14;">`publish`</span>.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">Use this to check that tarball is well structured and contains all needed files, before you publish.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">Good way to test it is to run <span class="sb" style="color: #d14;">`sudo pip install dist/edlib-*.tar.gz`</span>, which will try to install edlib from it, same way as pip will do it when it is published.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="sb" style="color: #d14;">`make clean`</span> removes all generated files.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">README.rst is auto-generated from <span class="p">[</span><span class="nv" style="color: #008080;">README-tmpl.rst</span><span class="p">](</span><span class="sx" style="color: #d14;">./README-tmpl.rst</span><span class="p">)</span>, to run regeneration do <span class="sb" style="color: #d14;">`make README.rst`</span>.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">README.rst is also automatically regenerated when building package (e.g. <span class="sb" style="color: #d14;">`make build`</span>).</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">This enables us to always have up to date results of code execution and help documentation of edlib methods in readme.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Publishing</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">Remember to update version in setup.py before publishing.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">To trigger automatic publish to PyPI, create a tag and push it to Github -> Travis will create sdist, build wheels, and push them all to PyPI while publishing new version.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">You can also publish new version manually if needed: run <span class="sb" style="color: #d14;">`make publish`</span> to create a source distribution and publish it to the PyPI.</span></pre>
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<li id="d803585b4b13aaa3cd9aa4aaf2fe7e5797750da5">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#d803585b4b13aaa3cd9aa4aaf2fe7e5797750da5"><strong>bindings/python/cedlib.pxd</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">@@ -12,11 +12,11 @@ cdef extern from "edlib.h" nogil:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">EdlibAlignMode</span> <span class="n" style="color: #333;">mode</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">EdlibAlignTask</span> <span class="n" style="color: #333;">task</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">additionalEqualitiesLength</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cython"> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="nf" style="color: #900; font-weight: 600;">edlibNewAlignConfig</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">EdlibAlignMode</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">EdlibAlignTask</span> <span class="n" style="color: #333;">task</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cython"> <span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">additionalEqualitiesLength</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cython"> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="nf" style="color: #900; font-weight: 600;">edlibDefaultAlignConfig</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cython"></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#0b5ebd1e73a970a851ab0b430b0efe417881144d"><strong>bindings/python/edlib.pyx</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">@@ -32,30 +32,27 @@ def _map_to_bytes(query, target, additional_equalities):</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cython"> <span class="n" style="color: #333;">query_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">_map_ascii_string</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cython"> <span class="n" style="color: #333;">target_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">_map_ascii_string</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cython"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NeedsAlphabetMapping</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Map non-ascii symbols into an ASCII alphabet so it can be used</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># in the C++ code</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cython"> <span class="n" style="color: #333;">query_vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cython"> <span class="n" style="color: #333;">target_vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cython"> <span class="n" style="color: #333;">input_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cython"> <span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">query_vals</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">union</span><span class="p">(</span><span class="n" style="color: #333;">target_vals</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cython"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">input_mapping</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">256</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Map elements of alphabet to chars from 0 up to 255, so that Edlib can work with them,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># since C++ Edlib needs chars.</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cython"> <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">union</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">256</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cython"> <span class="s" style="color: #d14;">"query and target combined have more than 256 unique values, "</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cython"> <span class="s" style="color: #d14;">"this is not supported."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cython"> <span class="n" style="color: #333;">map_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">input_mapping</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cython"> <span class="n" style="color: #333;">alphabet_to_byte_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cython"> <span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="n" style="color: #333;">idx</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">byteorder</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'big'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cython"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cython"> <span class="n" style="color: #333;">map_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span> <span class="sa">b</span><span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">alphabet_to_byte_mapping</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cython"> <span class="n" style="color: #333;">query_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">map_seq</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cython"> <span class="n" style="color: #333;">target_bytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">map_seq</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">additional_equalities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cython"> <span class="n" style="color: #333;">additional_equalities</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cython"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">input_mapping</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">input_mapping</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cython"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">alphabet_to_byte_mapping</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">].</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'utf-8'</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">alphabet_to_byte_mapping</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="p"><span class="idiff">].</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'utf-8'</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">additional_equalities</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">input</span>_mapping</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff right">input</span>_mapping</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">alphabet_to_byte</span>_mapping</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff right">alphabet_to_byte</span>_mapping</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">target_bytes</span><span class="p">,</span> <span class="n" style="color: #333;">additional_equalities</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cython"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">align</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NW"</span><span class="p">,</span> <span class="n" style="color: #333;">task</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"distance"</span><span class="p">,</span> <span class="n" style="color: #333;">k</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;">additionalEqualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cython"> <span class="s" style="color: #d14;">""" Align query with target using edit distance.</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cython"><span class="s" style="color: #d14;"> @param {str or bytes or iterable of hashable objects} query, combined with target must have no more</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">@@ -66,8 +63,8 @@ def align(query, target, mode="NW", task="distance", k=-1, additionalEqualities=</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'NW' for global (default)</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'HW' for infix</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'SHW' for prefix.</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cython"><span class="s" style="color: #d14;"> @param {string} task Optional. Tells edlib what to calculate. <span class="idiff left right">L</span>ess there is to calculate,</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cython"><span class="s" style="color: #d14;"> faster it is. Possible value are (from fastest to slowest):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cython"><span class="s" style="color: #d14;"> @param {string} task Optional. Tells edlib what to calculate. <span class="idiff left right">The l</span>ess there is to calculate,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cython"><span class="s" style="color: #d14;"> <span class="idiff left right">the </span>faster it is. Possible value are (from fastest to slowest):</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'distance' - find edit distance and end locations in target. Default.</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'locations' - find edit distance, end locations and start locations.</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cython"><span class="s" style="color: #d14;"> - 'path' - find edit distance, start and end locations and alignment path.</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">@@ -81,8 +78,8 @@ def align(query, target, mode="NW", task="distance", k=-1, additionalEqualities=</td>
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81
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cython"><span class="s" style="color: #d14;"> characters to act as a wildcards.</span></span>
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82
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cython"><span class="s" style="color: #d14;"> Set to None (default) if you do not want to extend edlib's default equality definition.</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cython"><span class="s" style="color: #d14;"> @return Dictionary with following fields:</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cython"><span class="s" style="color: #d14;"> {int} editDistance -1 if it is larger than k.</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cython"><span class="s" style="color: #d14;"> {int} alphabetLength</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cython"><span class="s" style="color: #d14;"> {int} editDistance <span class="idiff left right">Integer, </span>-1 if it is larger than k.</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cython"><span class="s" style="color: #d14;"> {int} alphabetLength<span class="idiff left right"> Integer, length of unique characters in 'query' and 'target'</span></span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cython"><span class="s" style="color: #d14;"> {[(int, int)]} locations List of locations, in format [(start, end)].</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cython"><span class="s" style="color: #d14;"> {string} cigar Cigar is a standard format for alignment path.</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cython"><span class="s" style="color: #d14;"> Here we are using extended cigar format, which uses following symbols:</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">@@ -112,15 +109,17 @@ def align(query, target, mode="NW", task="distance", k=-1, additionalEqualities=</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">tmp_bytes</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_cstring</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">cedlib</span><span class="p">.</span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">c_additionalEqualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">additionalEqualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualitiesLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cython"> <span class="n" style="color: #333;">c<span class="idiff left">config</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">additionalEqualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cedlib</span><span class="p">.</span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*></span> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Malloc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cython"> <span class="n" style="color: #333;">c<span class="idiff left right">_</span>additionalEqualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cedlib</span><span class="p">.</span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*></span> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Malloc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cython"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">cedlib</span><span class="p">.</span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">c_additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">c_additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">additionalEqualities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_additionalEqualities</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cython"> <span class="n" style="color: #333;">cconfig</span><span class="p">.</span><span class="n" style="color: #333;">additionalEqualitiesLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Run alignment -- need to get len before disabling the GIL</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" 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="127" 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">@@ -128,7 +127,7 @@ def align(query, target, mode="NW", task="distance", k=-1, additionalEqualities=</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cython"> <span class="n" style="color: #333;">target_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cython"> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">nogil</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cython"> <span class="n" style="color: #333;">cresult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cedlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">edlibAlign</span><span class="p">(</span><span class="n" style="color: #333;">cquery</span><span class="p">,</span> <span class="n" style="color: #333;">query_len</span><span class="p">,</span> <span class="n" style="color: #333;">ctarget</span><span class="p">,</span> <span class="n" style="color: #333;">target_len</span><span class="p">,</span> <span class="n" style="color: #333;">cconfig</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c<span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">additionalEqualities</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="n" style="color: #333;">c<span class="idiff">config</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">additionalEqualities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c<span class="idiff left">_</span>additionalEqualities</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="n" style="color: #333;">c<span class="idiff right">_</span>additionalEqualities</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cresult</span><span class="p">.</span><span class="n" style="color: #333;">status</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="LC133" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"There was an error."</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#2e7a0fef25a0e8843f022bc1badfb3500ec31fa3"><strong>bindings/python/setup.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">@@ -17,17 +17,20 @@ if USE_CYTHON:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">edlib_module_src</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"edlib.bycython.cpp"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Load README into long description.</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">here</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">here</span><span class="p">,</span> <span class="s" style="color: #d14;">'README.rst'</span><span class="p">),</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Load README.rst into long description.</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># User can skip using README.rst as long description: EDLIB_OMIT_README_RST=1 python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">OMIT_README_RST</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">'EDLIB_OMIT_README_RST'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">OMIT_README_RST</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">here</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">here</span><span class="p">,</span> <span class="s" style="color: #d14;">'README.rst'</span><span class="p">),</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Information</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"edlib"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" 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;">"1.3.<span class="idiff left right">6</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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;">"1.3.<span class="idiff left right">8.post2</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://github.com/Martinsos/edlib"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Martin Sosic"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"sosic.martin@gmail.com"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#b5e6d11fcc717483c4899727643243571563908e"><strong>bindings/python/test.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">@@ -68,6 +68,17 @@ testFailed = testFailed or (not (result and result["editDistance"] == 0))</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edlib</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="s" style="color: #d14;">"telephone"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SHW"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"><span class="n" style="color: #333;">testFailed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">testFailed</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">"editDistance"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">9</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Unicode characters</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edlib</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="s" style="color: #d14;">"ты милая"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ты гений"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="n" style="color: #333;">testFailed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">testFailed</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">"editDistance"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">"alphabetLength"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">12</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Long alphabet.</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="n" style="color: #333;">long_alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">257</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">long_seq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_alphabet</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="n" style="color: #333;">long_seq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_alphabet</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">long_alphabet</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">long_alphabet</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edlib</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">long_seq1</span><span class="p">,</span> <span class="n" style="color: #333;">long_seq2</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="n" style="color: #333;">testFailed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">testFailed</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">"editDistance"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">256</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">testFailed</span><span class="p">:</span></span>
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72
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Some of the tests failed!"</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libedlib (1.2.7-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Repository-Browse.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Remove obsolete field Name from debian/upstream/metadata (already present in</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> machine-readable debian/copyright).</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Apply multi-arch hints.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> + libedlib-dev, libedlib0, python3-edlib: Add Multi-Arch: same.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * d/watch: Add filemangle</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Upstream decided to use SOVERSION 1 - so follow this decision</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Install cmake files</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 13 Oct 2021 15:32:00 +0200</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">libedlib (1.2.6-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> d-shlibs,</span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -11,16 +11,18 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libedlib</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libedlib.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/Martinsos/edlib</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Package: libedlib<span class="idiff left right">0</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Package: libedlib<span class="idiff left right">1</span></span>
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20
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Multi-Arch: same</span>
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24
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: library for sequence alignment using edit distance</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> A lightweight and super fast C/C++ library for sequence alignment using</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> edit distance.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" 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="55" 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">@@ -53,7 +55,8 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> libedlib0 (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> libedlib1 (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Description: library for sequence alignment using edit distance (devel)</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> A lightweight and super fast C/C++ library for sequence alignment using</span>
</pre>
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59
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> edit distance.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" 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="88" 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">@@ -85,7 +88,7 @@ Package: edlib-aligner</td>
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85
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"> libedlib<span class="idiff left right">0</span> (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> libedlib<span class="idiff left right">1</span> (= ${binary:Version})</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">Description: edlib sequence alignment tool using edit distance</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> Edlib is a lightweight and super fast C/C++ library for sequence</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> alignment using edit distance. This package provides an aligner</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">@@ -114,6 +117,7 @@ Section: python</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">Description: library for sequence alignment using edit distance (Python3 module)</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> A lightweight and super fast C/C++ library for sequence alignment using</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"> edit distance.</span>
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<li id="c5b12eedcbfaeb489795a3c470454f1eea540ffb">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#c5b12eedcbfaeb489795a3c470454f1eea540ffb"><strong>debian/patches/cython3.patch</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">@@ -4,20 +4,34 @@ Description: Use Cython3/Python3</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/bindings/python/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bindings/python/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">7,15 +7,15</span> @@</span> edlib: ../../edlib</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> cp -<span class="idiff left right">R</span> ../../edlib .</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">6,8 +6,7</span> @@</span> edlib: <span class="idiff">$(shell find </span>../../edlib<span class="idiff right">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> <span class="idiff left">rm -rf edlib && </span>cp -<span class="idiff right">r</span> ../../edlib .</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> pyedlib.bycython.cpp: edlib.pyx cedlib.pxd</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python -m pip install cython</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cython --cplus edlib.pyx -o edlib.bycython.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cython3 --cplus edlib.pyx -o edlib.bycython.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> #######################################</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> ############## COMMANDS ###############</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> build: ${FILES}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # To build package, README.rst is needed, because it goes into long description of package,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # which is what is visible on PyPI.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -18,19 +17,18 @@</span> pyedlib.bycython.cpp: edlib.pyx cedlib.p</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> BUILD_SOURCE_FILES=edlib pyedlib.bycython.cpp setup.py</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> buildWithoutREADME.rst: ${BUILD_SOURCE_FILES}</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EDLIB_OMIT_README_RST=1 python setup.py build_ext -i</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EDLIB_OMIT_README_RST=1 python3 setup.py build_ext -i</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> README.rst: buildWithoutREADME.rst README-tmpl.rst</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python -m pip install cogapp</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> cog -d -o README.rst README-tmpl.rst </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> BUILD_FILES=${BUILD_SOURCE_FILES} README.rst</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> build: ${BUILD_FILES}</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build_ext -i</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py build_ext -i</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> sdist: <span class="idiff left right">${FILES}</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> sdist: <span class="idiff left right">edlib pyedlib.bycython.cpp setup.py README.rst MANIFEST.in</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py sdist</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py sdist</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> </span>
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<li id="64b13b88ce64948b10e3d8c03b0badd31684a749">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#64b13b88ce64948b10e3d8c03b0badd31684a749"><strong>debian/patches/enable_shared_and_static.patch</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">@@ -4,7 +4,7 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-01-08</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">4</span>,9 +1<span class="idiff">4</span>,6 @@</span> set(CMAKE_CXX_STANDARD 1<span class="idiff right">1</span>)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">8</span>,9 +1<span class="idiff">8</span>,6 @@</span> set(CMAKE_CXX_STANDARD 1<span class="idiff right">4</span>)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> set(CMAKE_CXX_STANDARD_REQUIRED ON) # Falling back to different standard it not allowed.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> set(CMAKE_CXX_EXTENSIONS OFF) # Make sure no compiler-specific features are used.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </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">@@ -14,7 +14,7 @@ Last-Update: 2021-01-08</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # Set strict warnings.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> if(MSVC)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> # Force to always compile with W4</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">47</span>,7 +4<span class="idiff right">4</span>,13 @@</span> set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMA</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">51</span>,7 +4<span class="idiff right">8</span>,13 @@</span> set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMA</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> file(GLOB SOURCES "edlib/src/*.cpp")</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> # Create libraries.</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">@@ -26,21 +26,24 @@ Last-Update: 2021-01-08</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/edlib/include></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $<INSTALL_INTERFACE:include>)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> add_library(edlib::edlib ALIAS edlib)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> set_target_properties(edlib</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> <span class="idiff left right"> </span>PROPERTIES</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="idiff left right"> VERSION ${PROJECT_VERSION}</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="p"><span class="idiff left">@@ -71,12 +74,12 @@</span></span><span class="idiff right"> endif(</span>)</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> <span class="idiff left right">if (NOT WIN32) # If on windows, do not build binaries that do not support windows.</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> <span class="idiff left right">add_executable(edlib-aligner apps/aligner/aligner.cpp</span>)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> target_link_libraries(edlib-aligner edlib)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left">+</span> <span class="idiff right">target_link_libraries(edlib-aligner edlib_static</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> PROPERTIES</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p"><span class="idiff left">@@ -87,7 +90,7 @@</span></span><span class="idiff right"> endif()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="idiff left right"> if(EDLIB_BUILD_UTILITIES</span>)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> <span class="idiff left right"> if(NOT WIN32) # If on windows, do not build binaries that do not support windows.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> <span class="idiff left right"> add_executable(edlib-aligner apps/aligner/aligner.cpp)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left">- </span> <span class="idiff right">target_link_libraries(edlib-aligner edlib</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left">+ </span> target_link_libraries(edlib-aligner edlib<span class="idiff right">_static</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> <span class="idiff left right"> endif(</span>)</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> endif()</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> # Create target 'install' for installing libraries.</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install(TARGETS edlib DESTINATION ${CMAKE_INSTALL_LIBDIR})</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS edlib edlib_static DESTINATION ${CMAKE_INSTALL_LIBDIR})</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> install(FILES edlib/include/edlib.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> # configure and install pkg-config file</span></pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -136,7 +139,7 @@</span> if(EDLIB_ENABLE_INSTALL)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> # Create target 'install' for installing libraries.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> install(</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- TARGETS edlib</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ TARGETS edlib edlib_static</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> EXPORT ${targets_export_name} </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}</span></pre>
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<li id="48e6df23def433866728dc58dedbaa6ffaddc0e4">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#48e6df23def433866728dc58dedbaa6ffaddc0e4"><strong>debian/patches/really_exclude_readme.rst.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 13 Oct 2021 11:51:04 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: After trying lots of ways to specify EDLIB_OMIT_README_RST environtment variable</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> None worked - thus patching it out here</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/bindings/python/setup.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bindings/python/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span> else:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # Load README.rst into long description.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # User can skip using README.rst as long description: EDLIB_OMIT_README_RST=1 python setup.py install</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-OMIT_README_RST = os.getenv('EDLIB_OMIT_README_RST', False)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+OMIT_README_RST = True # os.getenv('EDLIB_OMIT_README_RST', False)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> if not OMIT_README_RST:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> here = os.path.abspath(os.path.dirname(__file__))</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> with open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">soversion.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">do_not_build_hello_example.patch</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right"># </span>soversion.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right"># </span>do_not_build_hello_example.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">cython3.patch</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># signed_char.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">enable_shared_and_static.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">really_exclude_readme.rst.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#b8c83f631c612dd39b6cbd8b440b068ed61a1b27"><strong>debian/patches/signed_char.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Declare characters signed explicitly</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/911967</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://stackoverflow.com/questions/31634962/narrowing-conversion-from-int-to-char-inside-for-legal-values-when-cro</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: Wed, 19 Dec 2018 12:09:52 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- a/test/runTests.cpp</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/runTests.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -412,12 +412,12 @@</span> bool test10() {</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> bool test11() {</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> int queryLength = 8;</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> int targetLength = 8;</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char query[8] = {-127, 127, -55, 0, 42, 0, 127, -55};</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char target[8] = {-127, 127, 0, 42, 0, -55, 127, 42};</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char query[8] = {-127, 127, -55, 0, 42, 0, 127, -55};</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char target[8] = {-127, 127, 0, 42, 0, -55, 127, 42};</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bool r = executeTest(query, queryLength, target, targetLength, EDLIB_MODE_HW);</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r = r && executeTest(query, queryLength, target, targetLength, EDLIB_MODE_NW);</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r = r && executeTest(query, queryLength, target, targetLength, EDLIB_MODE_SHW);</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bool r = executeTest((char *)query, queryLength, (char *)target, targetLength, EDLIB_MODE_HW);</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r = r && executeTest((char *)query, queryLength, (char *)target, targetLength, EDLIB_MODE_NW);</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r = r && executeTest((char *)query, queryLength, (char *)target, targetLength, EDLIB_MODE_SHW);</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> return r;</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -6,7 +6,11 @@ export PYBUILD_NAME = edlib</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release \</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -DEDLIB_BUILD_EXAMPLES=False \</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -DBUILD_TESTING=False \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -DEDLIB_OMIT_README_RST=1</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">EDLIB_OMIT_README_RST=1</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh $@ --with python3</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">@@ -17,8 +21,8 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_auto_build --buildsystem=cmake</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> # $(MAKE) --directory=bindings/python</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> $(MAKE) --directory=bindings/python edlib pyedlib.bycython.cpp</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh_auto_build --buildsystem=pybuild -- --dir bindings/python</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">EDLIB_OMIT_README_RST=1 </span>$(MAKE) --directory=bindings/python edlib pyedlib.bycython.cpp</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> <span class="idiff left right">EDLIB_OMIT_README_RST=1 </span>dh_auto_build --buildsystem=pybuild -- --dir bindings/python</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> dh_auto_install --buildsystem=cmake</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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">@@ -33,6 +37,7 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> --devunversioned \</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> --exclude-la \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> --movedev debian/tmp/usr/include/* usr/include \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> --movedev debian/tmp/usr/lib/*/cmake usr/lib/$(DEB_HOST_MULTIARCH) \</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> --movedev debian/tmp/usr/lib/*/pkgconfig usr/lib/$(DEB_HOST_MULTIARCH) \</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> debian/tmp/usr/lib/*/*.so</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" 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="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Name: edlib</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/Martinsos/edlib/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/Martinsos/edlib/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Entry: edlib</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">@@ -6,3 +7,5 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Entry: OMICS_15611</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/Martinsos/edlib.git</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Repository-Browse: https://github.com/Martinsos/edlib</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/Martinsos/edlib/releases .*/archive/v@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/Martinsos/edlib/releases .*/v@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#3feb5d4b34b40244aace1454513fbdd04f498996"><strong>edlib-config.cmake.in</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@PACKAGE_INIT@</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">include(${CMAKE_CURRENT_LIST_DIR}/@targets_export_name@.cmake)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">check_required_components(edlib)</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#250a624cf61d30af86e091990ce36ef46bcd0b59"><strong>edlib.pc.in</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">libdir=@CMAKE_INSTALL_FULL_LIBDIR@</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@</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">Name: <span class="idiff left right">E</span>dlib</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Name: <span class="idiff left right">e</span>dlib</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Description: Lightweight and super fast C/C++ library for sequence alignment using edit distance</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Version: @edlib_VERSION@</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Libs: -L${libdir} -ledlib</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Cflags: -I${includedir}</span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Cflags: -I${includedir}<span class="idiff left right"> @PKG_EDLIB_DEFS@</span></span></pre>
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<li id="1a7726f53bb6b76561c94b784c9e79695b9b074e">
<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#1a7726f53bb6b76561c94b784c9e79695b9b074e"><strong>edlib/include/edlib.h</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">@@ -7,6 +7,21 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Main header file, containing all public functions and structures.</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Define EDLIB_API macro to properly export symbols</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef EDLIB_SHARED</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef _WIN32</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef EDLIB_BUILD</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EDLIB_API __declspec(dllexport)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EDLIB_API __declspec(dllimport)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EDLIB_API __attribute__ ((visibility ("default")))</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EDLIB_API</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -115,7 +130,7 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * or e.g. if you want edlib to be case insensitive.</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Can be set to NULL if there are none.</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Number of additional equalities, which is non-negative number.</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">@@ -128,15 +143,17 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Helper method for easy construction of configuration object.</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return Configuration object filled with given parameters.</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">edlibNewAlignConfig</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignMode</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignTask</span> <span class="n" style="color: #333;">task</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">additionalEqualitiesLength</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">EDLIB_API</span> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">edlibNewAlignConfig</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignMode</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignTask</span> <span class="n" style="color: #333;">task</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">additionalEqualitiesLength</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return Default configuration object, with following defaults:</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * k = -1, mode = EDLIB_MODE_NW, task = EDLIB_TASK_DISTANCE, no additional equalities.</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">edlibDefaultAlignConfig</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">EDLIB_API</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">edlibDefaultAlignConfig</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -204,7 +221,7 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Frees memory in EdlibAlignResult that was allocated by edlib.</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * If you do not use it, make sure to free needed members manually using free().</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">edlibFreeAlignResult</span><span class="p">(</span><span class="n" style="color: #333;">EdlibAlignResult</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">EDLIB_API</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">edlibFreeAlignResult</span><span class="p">(</span><span class="n" style="color: #333;">EdlibAlignResult</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -222,9 +239,11 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return Result of alignment, which can contain edit distance, start and end locations and alignment path.</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Make sure to clean up the object using edlibFreeAlignResult() or by manually freeing needed members.</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">EdlibAlignResult</span> <span class="n" style="color: #333;">edlibAlign</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">config</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">EDLIB_API</span> <span class="n" style="color: #333;">EdlibAlignResult</span> <span class="n" style="color: #333;">edlibAlign</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -246,10 +265,10 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Needed memory is allocated and given pointer is set to it.</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Do not forget to free it later using free()!</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">edlibAlignmentToCigar</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignment</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignmentLength</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">EdlibCigarFormat</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cigarFormat</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">EDLIB_API</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">edlibAlignmentToCigar</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignment</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignmentLength</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c"> <span class="n" style="color: #333;">EdlibCigarFormat</span> <span class="n" style="color: #333;">cigarFormat</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="c"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/libedlib/-/compare/8fc55699d3031e09e1f60db87d4c288a11e7c012...9fe8873554cb4607bd8e8e864e2eb3db97f34761#99b7f95ca57c5f3e70bca1d739cd0f9cce7b542e"><strong>edlib/src/edlib.cpp</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">@@ -361,7 +361,7 @@ static inline Word* buildPeq(const int alphabetLength,</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">Word</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Peq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Word</span><span class="p">[(</span><span class="n" style="color: #333;">alphabetLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumBlocks</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Build Peq (1 is match, 0 is mismatch). NOTE: last column is wildcard(symbol that matches anything) with just 1s</span></span>
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<pre style="margin: 0;">-<span id="LC364" 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;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">char</span></span> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alphabetLength</span><span class="p">;</span> <span class="n" style="color: #333;">symbol</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC364" 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;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">alphabetLength</span><span class="p">;</span> <span class="n" style="color: #333;">symbol</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC365" 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;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxNumBlocks</span><span class="p">;</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alphabetLength</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">Peq</span><span class="p">[</span><span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumBlocks</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><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">@@ -1460,7 +1460,7 @@ static string transformSequences(const char* const queryOriginal, const int quer</td>
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</span> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="nf" style="color: #900; font-weight: 600;">edlibNewAlignConfig</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignMode</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">EdlibAlignTask</span> <span class="n" style="color: #333;">task</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1463" class="line" lang="cpp"> <span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">EdlibEqualityPair</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">additionalEqualities</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">additionalEqualitiesLength</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="cpp"> <span class="n" style="color: #333;">EdlibAlignConfig</span> <span class="n" style="color: #333;">config</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="cpp"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">project(</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> 'edlib',</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> 'cpp', 'c',</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> version : '1.2.6',</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> default_options : [</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> 'buildtype=release',</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> 'warning_level=3',</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 'cpp_std=c++14',</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> 'b_ndebug=if-release',</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> 'default_library=static'</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ],</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> license : 'MIT',</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> meson_version : '>= 0.52.0',</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">project_version_major = meson.project_version().split('.')[0]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">###### Libraries ######</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">edlib_lib_compile_args = ['-DEDLIB_BUILD']</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">if get_option('default_library') != 'static'</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> edlib_lib_compile_args += ['-DEDLIB_SHARED']</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># If default_library == 'static', library() builds and returns static library.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># If default_library == 'shared', library() builds and returns shared library.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># If default_library == 'both', library() builds both static and shared libraries,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"># but only shared one is returned as value and therefore used in the rest of the build.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">if (get_option('default_library') == 'both')</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> error('\'both\' as a value for default_library option is not supported because it would'</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> + ' build static library with shared library flags, exporting symbols!'</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> + 'Instead, build twice, once with \'static\' and once with \'shared\'.')</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">edlib_lib = library('edlib',</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> sources : files(['edlib/src/edlib.cpp']),</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> include_directories : include_directories('edlib/include'),</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> dependencies : [],</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> install : true,</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> cpp_args : edlib_lib_compile_args,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> gnu_symbol_visibility : 'inlineshidden',</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> soversion : project_version_major # Used only for shared library.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">edlib_dep = declare_dependency(</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> include_directories : include_directories('edlib/include'),</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> link_with : edlib_lib,</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> compile_args : edlib_lib_compile_args</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">###### Executables ######</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">hello_main = executable(</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> 'hello-world',</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> files(['apps/hello-world/helloWorld.c']),</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> dependencies : [edlib_dep],</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">)</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">if build_machine.system() != 'windows'</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> aligner_main = executable(</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> 'edlib-aligner',</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> files(['apps/aligner/aligner.cpp']),</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> dependencies : [edlib_dep],</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> install : true,</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> )</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">runTests_main = executable(</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> 'runTests',</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> files(['test/runTests.cpp']),</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> dependencies : [edlib_dep],</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> include_directories : include_directories('test'),</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">)</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">###### Tests ######</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">test('runTests', runTests_main)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">test('hello', hello_main)</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">if build_machine.system() != 'windows'</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> test('aligner', aligner_main,</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> args : [</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> files('apps/aligner/test_data/query.fasta',</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> 'apps/aligner/test_data/target.fasta'),</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> ],</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> )</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">endif</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">###### Install ######</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">install_headers('edlib/include/edlib.h')</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">pkg = import('pkgconfig')</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">pkg.generate(edlib_lib,</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> name: 'edlib',</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> url: 'https://github.com/Martinsos/edlib',</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> filebase : 'edlib-' + project_version_major,</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> extra_cflags : edlib_lib_compile_args,</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> description : 'Lightweight and super fast C/C++ library for sequence alignment using edit distance',</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">)</span></pre>
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