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<h3>
Martin Uecker pushed to branch master
at <a href="https://salsa.debian.org/med-team/bart">Debian Med / bart</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bart/commit/080f51d3d770cb529bee54b464e3ec3578318213">080f51d3</a></strong>
<div>
<span>by Martin Uecker</span>
<i>at 2018-12-11T18:52:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">include some fixes from upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bart/commit/90ee9e5b53696a5b2f2ea2f8bbdf591eb1747072">90ee9e5b</a></strong>
<div>
<span>by Martin Uecker</span>
<i>at 2018-12-11T19:05:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deactivate ode unit test (fails on some archs)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bart/commit/3663f8fa7c374fd9ed2ac2469a970b5b910bbdf0">3663f8fa</a></strong>
<div>
<span>by Martin Uecker</span>
<i>at 2018-12-11T19:38:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">autopkgtest for octave interface script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bart/commit/5cb0edf1bbfe548a53813b917d0827b78a45d152">5cb0edf1</a></strong>
<div>
<span>by Martin Uecker</span>
<i>at 2018-12-11T21:15:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deactivate unit tests for some more archs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bart/commit/ba712eb51fa3b91b22d011a8dab67fc2edf87570">ba712eb5</a></strong>
<div>
<span>by Martin Uecker</span>
<i>at 2018-12-11T21:15:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#27e13624dc99f83ac3547f06c7f8e982153e1ce2">
<span class="new-file">
+
debian/patches/0001-some-more-memory-leaks.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#59f192a5928793c20b03da7a490844bc764d304a">
<span class="new-file">
+
debian/patches/0002-fix-bart-script.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#d71a27229b2906f68d8fc28beef22621f32b159b">
debian/patches/0003-relax-unit-test.patch
</a>
</li>
<li class="file-stats">
<a href="#4a47a40ee00cf935b016989a0905ddc91300c0c5">
debian/patches/0001-makefile-change-for-compatibility-with-debian.patch
→
debian/patches/0004-makefile-change-for-compatibility-with-debian.patch
</a>
</li>
<li class="file-stats">
<a href="#d0b2c4b61bd2c93562a77914632d55761092645f">
debian/patches/0002-remove-empty-directory.patch
→
debian/patches/0005-remove-empty-directory.patch
</a>
</li>
<li class="file-stats">
<a href="#31462d023c842ec57522cb252c9566937db27ecb">
<span class="new-file">
+
debian/patches/0006-deactivate-ode-unit-tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#0e904c54e7a553e8e74aed0c6ca42a07d4c97009">
<span class="new-file">
+
debian/tests/octave-integration
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bart (0.4.04-1.1) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add some fixes from upstream.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Deactivate unit tests for ODE solver.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Deactivate unit tests for some archs.</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtest for octave interface script.</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Martin Uecker <martin.uecker@med.uni-goettingen.de> Tue, 11 Dec 2018 13:07:12 +0100</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">bart (0.4.04-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * New upstream version.</span>
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<li id="27e13624dc99f83ac3547f06c7f8e982153e1ce2">
<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#27e13624dc99f83ac3547f06c7f8e982153e1ce2"><strong>debian/patches/0001-some-more-memory-leaks.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Martin Uecker <martin.uecker@med.uni-goettingen.de></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Mon, 10 Dec 2018 21:32:53 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: some more memory leaks</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">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> src/noncart/nufft.c | 1 +</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> src/pics.c | 14 +++++---------</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 2 files changed, 6 insertions(+), 9 deletions(-)</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="gh" style="color: #999;">diff --git a/src/noncart/nufft.c b/src/noncart/nufft.c</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index ed0a6e4..2d9d6bc 100644</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/noncart/nufft.c</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;">+++ b/src/noncart/nufft.c</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -590,6 +590,7 @@ static void nufft_free_data(const linop_data_t* _data)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> md_free(data->fftmod);</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> md_free(data->weights);</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> md_free(data->roll);</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;">+ md_free(data->basis);</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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #ifdef USE_CUDA</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> md_free(data->linphase_gpu);</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/pics.c b/src/pics.c</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gh" style="color: #999;">index da6ce4b..38b7624 100644</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/pics.c</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/pics.c</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -79,20 +79,15 @@ static const struct linop_s* sense_nc_init(const long max_dims[DIMS], const long</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> */</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> const struct linop_s* fft_slice = linop_fft_create(DIMS, map_dims, SLICE_FLAG);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const struct linop_s* tmp = fft_op;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fft_op = linop_chain(fft_slice, tmp);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- linop_free(tmp);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- linop_free(fft_slice);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fft_op = linop_chain_FF(fft_slice, fft_op);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const struct linop_s* lop = linop_chain(maps_op, fft_op);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const struct linop_s* lop = linop_chain_FF(maps_op, fft_op);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> //precond_op[0] = (struct operator_s*) nufft_precond_create( fft_op );</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> precond_op[0] = NULL;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- linop_free(maps_op);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- linop_free(fft_op);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> return lop;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -414,7 +409,7 @@ int main_pics(int argc, char* argv[])</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> if (NULL != basis_file) {</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> const struct linop_s* basis_op = linop_fmac_create(DIMS, bmx_dims, COEFF_FLAG, TE_FLAG, ~(COEFF_FLAG | TE_FLAG), basis);</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- forward_op = linop_chain(forward_op, basis_op);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ forward_op = linop_chain_FF(forward_op, basis_op);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -677,6 +672,7 @@ int main_pics(int argc, char* argv[])</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> xfree(pat_file);</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> xfree(traj_file);</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ xfree(basis_file);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> double end_time = timestamp();</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span></pre>
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<li id="59f192a5928793c20b03da7a490844bc764d304a">
<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#59f192a5928793c20b03da7a490844bc764d304a"><strong>debian/patches/0002-fix-bart-script.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Martin Uecker <martin.uecker@med.uni-goettingen.de></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Tue, 11 Dec 2018 09:25:17 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: fix bart script</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">---</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> matlab/bart.m | 51 ++++++++++++++++++++++++++-------------------------</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 1 file changed, 26 insertions(+), 25 deletions(-)</span>
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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"><span class="gh" style="color: #999;">diff --git a/matlab/bart.m b/matlab/bart.m</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index 47d0af4..861a024 100644</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/matlab/bart.m</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;">+++ b/matlab/bart.m</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,23 +12,24 @@ function [varargout] = bart(cmd, varargin)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> end</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> bart_path = getenv('TOOLBOX_PATH');</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- isWSL = false;</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;">+ isWSL = false;</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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> if isempty(bart_path)</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if exist('/usr/local/bin/bart', 'file')</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> bart_path = '/usr/local/bin';</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> elseif exist('/usr/bin/bart', 'file')</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> bart_path = '/usr/bin';</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else </span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % Try to execute bart inside wsl, if it works, then it returns</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % status 0</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [bartstatus, ~] = system('wsl bart version -V');</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if bartstatus==0</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bart_path = '/usr/bin';</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- isWSL = true;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- error('Environment variable TOOLBOX_PATH is not set.');</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % Try to execute bart inside wsl, if it works, then it returns</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % status 0</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [bartstatus, ~] = system('wsl bart version -V');</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if bartstatus==0</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bart_path = '/usr/bin';</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ isWSL = true;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ error('Environment variable TOOLBOX_PATH is not set.');</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ end</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ end</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> end</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> % clear the LD_LIBRARY_PATH environment variable (to work around</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -60,20 +61,20 @@ function [varargout] = bart(cmd, varargin)</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> out_str = sprintf(' %s', out{:});</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if ispc</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if isWSL</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % For WSL and modify paths</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmdWSL = WSLPathCorrection(cmd);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- in_strWSL = WSLPathCorrection(in_str);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- out_strWSL = WSLPathCorrection(out_str); </span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ERR = system(['wsl bart ', cmdWSL, ' ', in_strWSL, ' ', out_strWSL]);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % For cygwin use bash and modify paths</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ERR = system(['bash.exe --login -c ', ...</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strrep(bart_path, filesep, '/'), ...</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '"', '/bart ', strrep(cmd, filesep, '/'), ' ', ...</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strrep(in_str, filesep, '/'), ...</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ' ', strrep(out_str, filesep, '/'), '"']);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if isWSL</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % For WSL and modify paths</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmdWSL = WSLPathCorrection(cmd);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ in_strWSL = WSLPathCorrection(in_str);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ out_strWSL = WSLPathCorrection(out_str);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ERR = system(['wsl bart ', cmdWSL, ' ', in_strWSL, ' ', out_strWSL]);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % For cygwin use bash and modify paths</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ERR = system(['bash.exe --login -c ', ...</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strrep(bart_path, filesep, '/'), ...</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '"', '/bart ', strrep(cmd, filesep, '/'), ' ', ...</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strrep(in_str, filesep, '/'), ...</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ' ', strrep(out_str, filesep, '/'), '"']);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ end</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> ERR = system([bart_path, '/bart ', cmd, ' ', in_str, ' ', out_str]);</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> end</span></pre>
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<li id="d71a27229b2906f68d8fc28beef22621f32b159b">
<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#d71a27229b2906f68d8fc28beef22621f32b159b"><strong>debian/patches/0003-relax-unit-test.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">From: Martin Uecker <martin.uecker@med.uni-goettingen.de></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Date: <span class="idiff left right">Mon, 10 Dec 2018 14:44:21</span> +0100</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: <span class="idiff left right">Tue, 11 Dec 2018 09:26:07</span> +0100</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Subject: relax unit test</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">---</span>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#4a47a40ee00cf935b016989a0905ddc91300c0c5"><strong>debian/patches/0001-makefile-change-for-compatibility-with-debian.patch</strong>
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<strong>debian/patches/0004-makefile-change-for-compatibility-with-debian.patch</strong>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#d0b2c4b61bd2c93562a77914632d55761092645f"><strong>debian/patches/0002-remove-empty-directory.patch</strong>
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<strong>debian/patches/0005-remove-empty-directory.patch</strong>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#31462d023c842ec57522cb252c9566937db27ecb"><strong>debian/patches/0006-deactivate-ode-unit-tests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Martin Uecker <martin.uecker@med.uni-goettingen.de></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Tue, 11 Dec 2018 20:04:44 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: deactivate ode unit tests</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">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> utests/test_ode_bloch.c | 12 ++++++------</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 1 file changed, 6 insertions(+), 6 deletions(-)</span>
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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"><span class="gh" style="color: #999;">diff --git a/utests/test_ode_bloch.c b/utests/test_ode_bloch.c</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index ce734bb..b7114e9 100644</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/utests/test_ode_bloch.c</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;">+++ b/utests/test_ode_bloch.c</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -86,7 +86,7 @@ static bool test_ode_bloch(void)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> return (err2 < 1.E-7);</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_ode_bloch);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_ode_bloch);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,7 +118,7 @@ static bool test_bloch_matrix(void)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> && (0. == out2[3]);</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_bloch_matrix);</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_bloch_matrix);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -147,7 +147,7 @@ static bool test_ode_matrix_bloch(void)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> return (err2 < 1.E-6);</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> }</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_ode_matrix_bloch);</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_ode_matrix_bloch);</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -222,7 +222,7 @@ static bool test_ode_sa(void)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> return err < 1.E-9;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_ode_sa);</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_ode_sa);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> static bool test_ode_sa2(void)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -286,7 +286,7 @@ static bool test_ode_sa2(void)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> return true;</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_ode_sa2);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_ode_sa2);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -342,4 +342,4 @@ static bool test_ode_sa_bloch(void)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-UT_REGISTER_TEST(test_ode_sa_bloch);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// UXT_REGISTER_TEST(test_ode_sa_bloch);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0001-<span class="idiff left right">makefile-change-for-compatibility-with-debian</span>.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">0002-<span class="idiff left right">remove-empty-directory</span>.patch</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0001-<span class="idiff left right">some-more-memory-leaks</span>.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">0002-<span class="idiff left right">fix-bart-script</span>.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">0003-relax-unit-test.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">0004-makefile-change-for-compatibility-with-debian.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">0005-remove-empty-directory.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">0006-deactivate-ode-unit-tests.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ DEB_BUILD_ARCH ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># Some tests fail on the following architectures probably</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># due to minor differences in floating point processing.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># For now, just turn it off...</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">NOTEST_ARCHS=<span class="idiff left right">i386 mips mipsel hurd-i386 kfreebsd-i386 m68k</span> sh4</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">NOTEST_ARCHS=<span class="idiff left right">armel armhf i386 mips mips64el mipsel hurd-i386 kfreebsd-i386 m68k powerpcspe</span> sh4</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh $@</span>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Test-Command: /usr/bin/bart version</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: bart</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">Tests: octave-integration</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Depends: octave-bart, octave</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/bart/compare/b06c93ecc5292c2940f5d8fe0efbb04dcc1e85d0...ba712eb51fa3b91b22d011a8dab67fc2edf87570#0e904c54e7a553e8e74aed0c6ca42a07d4c97009"><strong>debian/tests/octave-integration</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/octave-cli -qf</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bart('version');</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span></pre>
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