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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mrtrix3">Debian Med / mrtrix3</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/b0b5f88a4ab66003d90f17e697039c96fff5f764">b0b5f88a</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-28T22:53:51-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">packaging from mrtrix project
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/0688f71781092b161349cdb95b4af36d6a81fc92">0688f717</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-28T23:01:23-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initial tune ups for mrtrix3 package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/263976d161828922c2ff57e801441b4e0ea7fef8">263976d1</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-29T09:49:34-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tune rules to config,build,clean
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/966f350a5060ad0f6d70fa90c562cbef42ea6b52">966f350a</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-30T10:06:36-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial set of updates to build as mrtrix3 pkg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/319f37e4e282d42f62500902c530304194782eae">319f37e4</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-30T10:36:45-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">libeigen3 and opengl into b-depends, recommend numpy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/7872caadeb74558bae57eddd79e96cdbc2053c46">7872caad</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-30T16:01:57-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No extra priority
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/b67e8110c17772b346227f66e94725a2bfe544fc">b67e8110</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-08-30T22:07:43-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">a note
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/195e47d8d9c4d67c0664a8f37d2dc51d169078e3">195e47d8</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T13:08:43-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Symlink only mrview for now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/5f2616362cf6adeb5533ea2871a67ba7cf18538e">5f261636</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T13:10:13-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Python into dependencies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/51906a09fb0d1856cdb1bb23d2771e333daa5dc1">51906a09</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T13:11:36-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">And python2 explicitely since some scripts need python2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/31204e8f484c440f8a63e375bc9f4184e5fad027">31204e8f</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T19:39:09-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Various tune ups and placing under Debian Med umbrella
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/1ef673a173a67f48012d2b031638fed84e86891a">1ef673a1</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T19:39:52-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardening
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/022a0bf7b7c9a5a954d9730bae3f0ac85880e88c">022a0bf7</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T19:41:17-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/watch based on the one from mrtrix, thanks Andreas T
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/0666e46f767e5c44369fec9ecce3e75fff9b9455">0666e46f</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T20:02:08-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try enabling build time testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/1efc3191b30b2fc270e9be453c5eefb853c6e640">1efc3191</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T20:04:08-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">assure no online interactions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/e8952c54ce43a5812d31d6872ba6ce7b79f50936">e8952c54</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-04T22:26:55-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not use git to get test data, dump testing log if fail, need bc for tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/b4fb914a04cf026893993303a50334a82e1d1a5b">b4fb914a</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-05T09:19:35-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to provide CFLAGS for consistent operation across x86 platforms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/9a3aaec19a1403001aa4ce062e217dff21408092">9a3aaec1</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-05T09:57:17-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BF: project is under MPL-2.0 now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/a89cbaf00a22217d3d761fd88f4c4653b0059549">a89cbaf0</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-05T10:07:25-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lets upload to Debian proper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/9d491a2defea7563b18798e3cd11451be5baa100">9d491a2d</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-05T11:58:13-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed too old .dsc patches -- we do not build there any longer anyways
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/16e96112cc53bd19501add9c4ba48ec0722213f0">16e96112</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-09-07T16:25:23-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README.source to clarify source package generation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/ddf257bbbda777fea105e934c2496e5f8921accc">ddf257bb</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-11-21T23:08:20-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Need to disable PIE on older systems
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/1c6f44b54589a773c7fb3543990719ee42e20d12">1c6f44b5</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-12-13T12:55:33-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/gbp.conf - adjusted to relfect used branches layout, where debian branch is based on (original) upstream's master branch.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/610d7131a917fc01a6b4d2c69838dd90dc87a34f">610d7131</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-12-13T17:34:00-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge commit '3.0_RC3-135-g2b8e7d0c2' into debian
* commit '3.0_RC3-135-g2b8e7d0c2': (23 commits)
only include xmmintrin.h header if actually used
TravisCI: try using git repo to fetch Eigen
dwipreproc: Search PATH for 'eddy_cpu'
Streamline::calc_length(): Make no assumptions
dwipreproc: Compatibility with FSL6.0.0
_5ttgen/gif.py: Remove extraneous pylint directive
5ttgen GIF algorithm: fix for pylint errors
run_pylint: fix to report correct version information
run_pylint: log version information for potential debugging
MRView: fix translation in camera coordinates in screen capture tool
DICOM: be more lenient with slice timing vector is Siemens mosaics
mrtrix3.image.statistic(): Fix parameter naming
dwiextract: Fix extraction based on TRT
further updated test data for mrpad
merge updated test data for mrpad
mrpad: fix header translation of y and z axes
DICOM: increase resilience to errors and empty fields
mrview: fix -norealign option
dcminfo: fix -tags output
Fix bug json.load() -> json.loads()
...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/55474e9df2e25547b964a46d3a13c2f3f8c48ebd">55474e9d</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2018-12-13T17:34:18-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusted changelog entry for new snapshot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/825d39393e5186bf023168cf887635d63414c2a3">825d3939</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-07T11:38:23-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added patch changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff to "cherry-pick" 7fb509cf35d5862f073faaa7e136e987486960d9 (gl_core_3_3.h: simplify and fix typedefs)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/0f9168a2f053dd7dad5460a2d26f9f7e4dbd8b36">0f9168a2</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-07T11:38:32-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added patch changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff to "cherry-pick" 1c1d3304791bd029bca744ff6634bfa4824f6938 (gl_core_3_3.h: fix missing semicolon)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/d66ef42438f9ba7f6915c8cdd630e61a5e6694b6">d66ef424</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-07T11:42:44-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changelog entry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/61f0c969c1fb09fdb2c1637bd4aca0ae2b3f166c">61f0c969</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-07T11:44:36-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix symlinks for the manpages to point to mrtrix3.1.gz not the absent mrtrix.1.gz (Closes: #916775)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/556ad2a73deaadbec626fde2a29a311690529d4d">556ad2a7</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-21T23:38:00-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ship Python mrtrix3 module for internal use:
* Ship Python mrtrix3 module for internal use:
- Many tools rely on Python (2) support module, which was omitted
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/667393d799f372b966ad421bc948bece8487b548">667393d7</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-22T16:28:57-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up *.py? files upon install
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/45965c4fbb2877bb937fd56bd717249e22fa9cda">45965c4f</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-22T16:29:06-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/control, debian/patches/up_blend_python - just ask/use default Python (currently python2)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/45f43ce38955eefa55867df0d0cd531b1d97fad2">45f43ce3</a></strong>
<div>
<span>by Yaroslav Halchenko</span>
<i>at 2019-01-22T18:57:54-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Override dh_install instead of dh_auto_install for pruning .pyc files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/b3a5d28ebaacf89b848f0707bed13341e4dac4b2">b3a5d28e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-20T21:41:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag '3.0_rc3+git135-g2b8e7d0c2'
Update to upstream version '3.0~rc3+git135-g2b8e7d0c2'
with Debian dir e87262d348856b5bc9024c486bf3277ed938270f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrtrix3/commit/974ad5c338b7e0c65bd46c12aa83509ef5e8c008">974ad5c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-20T22:07:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Get the build at least starting
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
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<h4>Changes:</h4>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">MRtrix for Debian</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Packaging is based on the original one for mrtrix package, but now resides as</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">a branch on top of the upstream Git repository.</span>
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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">All MRtrix programs are installed in /usr/lib/mrtrix/bin (due to too generic</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">names of some of them, e.g. 'average'). You either have to call them with their</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">full path, or extend the search path by this directory. The MRtrix documentation</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">has information on how to do that for a number of popular environments. Please</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">note that it is not necessary to modify LD_LIBRARY_PATH -- despite the advice</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">in the MRtrix manual.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">For convenience, 'mrview' and other 'mr*' tools are directly avialable in</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">/usr/bin and 'mrview' is also listed in Desktop environment menus.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Note: conflicts known so far were discovered by</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"> $> for f in *; do echo "---- $f"; dlocate bin/$f; done</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ---- dirsplit</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> genisoimage: /usr/bin/dirsplit</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"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> -- Yaroslav Halchenko <debian@onerussian.com>, Thu, 30 Aug 2018 09:32:03 -0400</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Debian source package</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Debian source packages for new (possibly snapshot) releases are</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">generated using gbp buildpackage directly from Git repository, while</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">relying on settings within provided `debian/gbp.conf`. It is done so</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">to incorporate content of the test data which is provided within git</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">submodule under `testing/data`.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">pristine-tar is not used to store generated tarballs because of it not</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">supporting git submodules (yet) and thus resulting in large binary</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">deltas, ruining its utility.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Yaroslav Halchenko <debian@onerussian.com>, Fri, 7 Sep 2018 16:25:08 -0400</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-4) UNRELEASED; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * s/libqt4-opengl-dev/libqt5opengl5-dev/</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"> -- Andreas Tille <tille@debian.org> Mon, 20 Jan 2020 21:42:52 +0100</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">mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Clean up *.py? files upon install</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * debian/control, debian/patches/up_blend_python - just ask/use default</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Python (currently python2)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Yaroslav Halchenko <debian@onerussian.com> Tue, 22 Jan 2019 14:49:00 -0500</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">mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-2) neurodebian; urgency=medium</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"> * Picked up two commits from upstream's origin/simplify_gl_core_header</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> to resolve i386 build failure</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Fix symlinks for the manpages to point to mrtrix3.1.gz</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> not the absent mrtrix.1.gz (Closes: #916775)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> * Ship Python mrtrix3 module for internal use:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> - Many tools rely on Python (2) support module, which was omitted</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"> -- Yaroslav Halchenko <debian@onerussian.com> Mon, 21 Jan 2019 23:32:15 -0500</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">mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> * Fresh upstream snapshot</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> - potentially fixes FTBFS on some non-x32 platforms where failure was</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> due to the absent SSE support and xmmintrin.h</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> * debian/gbp.conf</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> - adjusted to relfect used branches layout, where debian branch is based on</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> (original) upstream's master branch.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> -- Yaroslav Halchenko <debian@onerussian.com> Thu, 13 Dec 2018 17:28:22 -0500</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">mrtrix3 (3.0~rc3+git86-g4b523b413-2) neurodebian; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * Need to disable PIE on older systems</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> -- Yaroslav Halchenko <debian@onerussian.com> Wed, 21 Nov 2018 23:08:01 -0500</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">mrtrix3 (3.0~rc3+git86-g4b523b413-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> * Initial packaging based on mrtrix package (Closes: #907978)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> * Initial packaging for mrtrix3 as a separate source package to</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> allow retaining (although with installation conflict) of both</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> 2 and 3 series</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"> -- Yaroslav Halchenko <debian@onerussian.com> Wed, 05 Sep 2018 10:07:15 -0400</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">9</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: mrtrix3</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@alioth-lists.debian.net></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Michael Hanke <mih@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Yaroslav Halchenko <debian@onerussian.com></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 9~),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> liboctave-dev,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libgsl-dev | libgsl0-dev,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libeigen3-dev,</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libqt5opengl5-dev,</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> qtbase5-dev-tools,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libqt5svg5-dev,</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> pkg-config,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libgtkmm-2.4-dev,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libgtkglext1-dev,</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> imagemagick,</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> libtiff-dev,</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> matlab-support-dev,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> bc,</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mrtrix3</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mrtrix3.git</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Homepage: http://www.mrtrix.org</span>
</pre>
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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">Package: mrtrix3</span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Architecture: any</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Section: science</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ${misc:Depends},</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python,</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Recommends: python-numpy</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Conflicts: mrtrix</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Suggests: mrtrix3-doc,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> octave,</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> matlab-support</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Description: diffusion-weighted MRI white matter tractography</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> Set of tools to perform diffusion-weighted MRI white matter tractography of the</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> brain in the presence of crossing fibres, using Constrained Spherical</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Package: mrtrix3-doc</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Conflicts: mrtrix-doc</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Description: documentation for mrtrix3</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> Set of tools to perform diffusion-weighted MRI white matter tractography of the</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> brain in the presence of crossing fibres, using Constrained Spherical</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> This package provides the documentation in HTML format.</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: MRtrix3</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Upstream-Contact: Donald Tournier <jdtournier@gmail.com></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Source: http://github.com/MRtrix3/mrtrix3</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" 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">Files: *</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Copyright: 2008-2018 the MRtrix3 contributors</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">License: MPL-2.0</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Files: core/file/json.h</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Copyright: 2013-2017 Niels Lohmann <http://nlohmann.me></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: MIT</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> of this software and associated documentation files (the "Software"), to deal</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> in the Software without restriction, including without limitation the rights</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> copies of the Software, and to permit persons to whom the Software is</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> furnished to do so, subject to the following conditions:</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> .</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> The above copyright notice and this permission notice shall be included in all</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> copies or substantial portions of the Software.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> SOFTWARE.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Copyright: 2010-2014, Michael Hanke <michael.hanke@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> 2018, Yaroslav Halchenko <debian@onerussian.com></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">License: MPL-2.0</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">License: MPL-2.0</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> On Debian systems the full text of the Mozilla Public License can be found</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> in the `/usr/share/common-licenses/MPL-2.0' file.</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#67df3adc98b97f87d2c73e4a05f22a987c3a5a7b"><strong>debian/gbp.conf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="conf">[<span class="n" style="color: #333;">DEFAULT</span>]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="conf"><span class="n" style="color: #333;">submodules</span> = <span class="n" style="color: #333;">True</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="conf"><span class="n" style="color: #333;">debian</span>-<span class="n" style="color: #333;">tag</span> = <span class="n" style="color: #333;">debian</span>/%(<span class="n" style="color: #333;">version</span>)<span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="conf"><span class="n" style="color: #333;">upstream</span>-<span class="n" style="color: #333;">tag</span> = %(<span class="n" style="color: #333;">version</span>)<span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="conf"><span class="n" style="color: #333;">upstream</span>-<span class="n" style="color: #333;">branch</span> = <span class="n" style="color: #333;">master</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="conf"><span class="n" style="color: #333;">debian</span>-<span class="n" style="color: #333;">branch</span> = <span class="n" style="color: #333;">debian</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="conf"></span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#2a78ead1a7c0455451afefd7d6930a14d1be3f1e"><strong>debian/mrtrix3-doc.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">html</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#4f2a78119d0e52ac55e8baa8b92a50ea208f80ec"><strong>debian/mrtrix3.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH MRTRIX "1" "April 2010" "MRtrix" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">MRtrix3 \- diffusion-weighted MRI white matter tractography</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">MRtrix is a set of tools to perform diffusion-weighted MRI white matter</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">tractography of the brain in the presence of crossing fibres, using Constrained</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SH "DEBIAN"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">All MRtrix programs are installed in /usr/lib/mrtrix/bin. You either have to</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">call them with their full path, or extend the search path by this directory.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">The MRtrix documentation has information on how to do that for a number of</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">popular environments. Please note that it is not necessary to modify</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">LD_LIBRARY_PATH -- despite the advice in the MRtrix manual.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SH "AUTHOR"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">MRtrix has been written by J\-Donald Tournier (d.tournier@brain.org.au)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">This manual page was written by Michael Hanke <michael.hanke@gmail.com>,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">for the Debian project (but may be used by others).</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">The full MRtrix user manual is provided by the mrtrix-doc package.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fBMRtrix Homepage:\fR http://www.mrtrix.org</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#121c1fb32133abe886395679b56d576405960bf6"><strong>debian/mrtrix3.desktop</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[Desktop Entry]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Encoding=UTF-8</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">GenericName=MRI Tractography View</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Name=MRview</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Exec=mrview %F</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">TryExec=mrview</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Type=Application</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Terminal=false</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;GTK;Viewer;</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Icon=mrtrix</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#a1bea5cde5937063b8c4a52cc9ad575cfd51c361"><strong>debian/mrtrix3.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">lib</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">so</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">icons</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">icons</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix</span><span class="o" style="font-weight: 600;">.</span><span class="nx">png</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pixmaps</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">desktop</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">applications</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="nx">matlab</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mrtrix3</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#aecb0233ec30ccf0f477c0cc6016389a4d2c2bf4"><strong>debian/mrtrix3.links</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mraverageheader usr/bin/mraverageheader</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mraverageheader.1.gz</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrcalc usr/bin/mrcalc</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcalc.1.gz</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrcat usr/bin/mrcat</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcat.1.gz</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrcheckerboardmask usr/bin/mrcheckerboardmask</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcheckerboardmask.1.gz</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrclusterstats usr/bin/mrclusterstats</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrclusterstats.1.gz</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrconvert usr/bin/mrconvert</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrconvert.1.gz</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrcrop usr/bin/mrcrop</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcrop.1.gz</span>
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrdegibbs usr/bin/mrdegibbs</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrdegibbs.1.gz</span>
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrdump usr/bin/mrdump</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrdump.1.gz</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mredit usr/bin/mredit</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mredit.1.gz</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrfilter usr/bin/mrfilter</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrfilter.1.gz</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrhistmatch usr/bin/mrhistmatch</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrhistmatch.1.gz</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrhistogram usr/bin/mrhistogram</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrhistogram.1.gz</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrinfo usr/bin/mrinfo</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrinfo.1.gz</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrmath usr/bin/mrmath</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrmath.1.gz</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrmetric usr/bin/mrmetric</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrmetric.1.gz</span>
</pre>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrpad usr/bin/mrpad</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrpad.1.gz</span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrregister usr/bin/mrregister</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrregister.1.gz</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrresize usr/bin/mrresize</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrresize.1.gz</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrstats usr/bin/mrstats</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrstats.1.gz</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrthreshold usr/bin/mrthreshold</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrthreshold.1.gz</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrtransform usr/bin/mrtransform</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrtransform.1.gz</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">usr/lib/mrtrix3/bin/mrview usr/bin/mrview</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrview.1.gz</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">/usr/share/mrtrix3/matlab /usr/share/matlab/site/m/mrtrix</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">/usr/share/mrtrix3/matlab /usr/share/octave/site/m/mrtrix</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mrtrix3.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: J-Donald Tournier <jdtournier@gmail.com></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: gl_core_3_3.h: fix missing semicolon</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">--- a/src/gui/opengl/gl_core_3_3.h</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/gui/opengl/gl_core_3_3.h</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -105,7 +105,7 @@</span> using GLchar = char;</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> using GLcharARB = char;</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #ifdef _WIN64</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-using GLintptr = signed long long int</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+using GLintptr = signed long long int;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #else</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> using GLintptr = signed long int;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> #endif</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#4b23c954edfec4c76d029bfde01c1ed9d25d11aa"><strong>debian/patches/changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff</strong></a>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#6d15fe81f050b10ce7b148e2f5751257d75a2c18"><strong>debian/patches/deb_run_tests</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_tests</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_tests</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -10,8 +10,7 @@</span> cat > $LOGFILE <<EOD</span>
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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"> EOD</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"><span class="gd" style="color: #000; background-color: #fdd;">-echo -n "fetching test data... "</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-git submodule update --init >> $LOGFILE 2>&1</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo -n "Debian build: Using available test data..." >> $LOGFILE</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if [ $? != 0 ]; then</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> echo ERROR!</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#deec4518f70256e25d849b2cfc2b3c34bd1a9da3"><strong>debian/patches/debian_build_cfg</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Change buildsystem setup for Debian</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Michael Hanke <michael.hanke@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -187,6 +187,15 @@</span> def pipe_errors_to_less_handler():</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> except:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> raise</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# honor the environment</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # the splitting is needed because the command is submitted as a list</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # and we need individual options -- it may not be that simple though...</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ env_flags = os.environ['LDFLAGS'].split()</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ld_flags.extend(env_flags)</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;">+ ld_lib_flags.extend(env_flags)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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19
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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"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">up_blend_python</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">deb_run_tests</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian_build_cfg</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#854db28855270f3283f803e3d0a9543de58613fb"><strong>debian/patches/up_blend_python</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/blend</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/blend</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#!/usr/bin/make -f</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -*- makefile -*-</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># get octave paths (have to build-depend on octave-headers)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/octave/debian/defs.make</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># same for Matlab</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/matlab/debian/defs.make</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># on older systems such as 16.04 PIE is not enabled by default and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># configure them fails # to link</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">DISABLE_HARDENING_OPTS</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> g++ <span class="nt" style="color: #000080;">-v</span> 2>&1 | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="nt" style="color: #000080;">-e</span> <span class="nt" style="color: #000080;">--enable-default-pie</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">",-pie"</span><span class="nf" style="color: #900; font-weight: 600;">)</span> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all<span class="nv" style="color: #008080;">$(DISABLE_HARDENING_OPTS)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># To avoid --match=native since wouldn't be supported on some platforms</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">CPP_MARCH</span><span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">DEB_HOST_ARCH</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_HOST_ARCH</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># guarantee the same precision on x86 platforms for tests</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(findstring z$(DEB_HOST_ARCH)z,zamd64z zi386z))</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="nt" style="color: #000080;">-mmmx</span> <span class="nt" style="color: #000080;">-msse</span> <span class="nt" style="color: #000080;">-msse2</span> <span class="nt" style="color: #000080;">-mfpmath</span><span class="o" style="font-weight: 600;">=</span>sse</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># To prevent any online interactions</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">http_proxy</span><span class="o" style="font-weight: 600;">=</span>http://127.0.0.1:9/</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">https_proxy</span><span class="o" style="font-weight: 600;">=</span>http://127.0.0.1:9/</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">QT_SELECT</span><span class="o" style="font-weight: 600;">=</span>qt5</span>
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28
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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">%</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"> dh <span class="nv" style="color: #008080;">$@</span></span>
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31
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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="nl">override_dh_auto_configure</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> ./configure <span class="nt" style="color: #000080;">-openmp</span> <span class="c" style="color: #998; font-style: italic;"># -debug</span></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">override_dh_auto_build</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"> ./build <span class="nt" style="color: #000080;">-verbose</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"><span class="nl">override_dh_install</span><span class="o" style="font-weight: 600;">:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"> dh_install</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># .pyc files get generated, so we remove all the .pyc/.pyo etc</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="p">-</span>find debian <span class="nt" style="color: #000080;">-iname</span> <span class="k" style="font-weight: 600;">*</span>.py? <span class="nt" style="color: #000080;">-delete</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"><span class="nl">override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="make"> ./run_tests <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">{</span> <span class="nb" style="color: #0086b3;">cat </span>testing.log<span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"><span class="nl">override_dh_link</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp </span>debian/mrtrix3.links.in debian/mrtrix3.links</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"> : <span class="c" style="color: #998; font-style: italic;"># Generate symlinks for all the mr* commands</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"> <span class="k" style="font-weight: 600;">for </span>f <span class="k" style="font-weight: 600;">in </span>debian/mrtrix3/usr/lib/mrtrix3/bin/mrview<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"> <span class="nv" style="color: #008080;">bn</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$$</span>f<span class="nf" style="color: #900; font-weight: 600;">)</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"usr/lib/mrtrix3/bin/</span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">bn usr/bin/</span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">bn"</span> <span class="o" style="font-weight: 600;">>></span> debian/mrtrix3.links<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"/usr/share/man/man1/mrtrix.1.gz /usr/share/man/man1/</span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">bn.1.gz"</span> <span class="o" style="font-weight: 600;">>></span> debian/mrtrix3.links<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"/usr/share/mrtrix3/matlab </span><span class="nv" style="color: #008080;">$(MATLAB_MDIR)</span><span class="s2" style="color: #d14;">/mrtrix"</span> <span class="o" style="font-weight: 600;">>></span> debian/mrtrix3.links</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"/usr/share/mrtrix3/matlab </span><span class="nv" style="color: #008080;">$(MDIR)</span><span class="s2" style="color: #d14;">/mrtrix"</span> <span class="o" style="font-weight: 600;">>></span> debian/mrtrix3.links</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="make"> dh_link</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># we want immediately useable docs and example data, they are in a dedicated</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># package already</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="make"><span class="nl">override_dh_compress</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="make"> dh_compress <span class="nt" style="color: #000080;">-X</span>.html</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="make"><span class="nl">override_dh_clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="make"> ./build clean</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="make"> find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s1" style="color: #d14;">'*.pyc'</span> <span class="nt" style="color: #000080;">-delete</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="make"> <span class="p">-</span><span class="nb" style="color: #0086b3;">rm </span>clean <span class="se" style="color: #d14;">\</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="make"> config configure.log build.log <span class="se" style="color: #d14;">\</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="make"> core/version.cpp lib/mrtrix3/_version.py src/exec_version.cpp</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="make"> dh_clean</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> debian/mrtrix.links</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="make"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="make"><span class="nl">override_dh_shlibdeps</span><span class="o" style="font-weight: 600;">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="make"> dh_shlibdeps <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$(CURDIR)</span>/lib</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</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">http://github.com/MRtrix3/mrtrix3/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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