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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/fast">Debian Med / fast</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/fast/commit/681f4ceb47d258845cab0412a1478b19bb210278">681f4ceb</a></strong>
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<span>by Shayan Doust</span>
<i>at 2019-08-11T07:32:14Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify some patch namings and disable NeuralNetwork tests
NeuralNetwork part of the test suite fails, so disable this for now. CMake now builds testFAST to which autopkgtest can call this.
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<h4>3 changed files:</h4>
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<a href="#82e0bda1ef781bbe11386f41bc18524910c179a4">
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+
debian/patches/fix_test.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#7c7a56b25cab05d40c3313c0d8a70f58caf600b0">
debian/patches/disable_tests.patch
→
debian/patches/set_cmake_options.patch
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<h4>Changes:</h4>
<li id="82e0bda1ef781bbe11386f41bc18524910c179a4">
<a href="https://salsa.debian.org/med-team/fast/commit/681f4ceb47d258845cab0412a1478b19bb210278#82e0bda1ef781bbe11386f41bc18524910c179a4"><strong>debian/patches/fix_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: hopefully temporary override to compile for tests</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This patch disables the test suite for NeuralNetwork as this is problematic. This needs checking.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-08-11</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Index: fast/source/FAST/Algorithms/NeuralNetwork/CMakeLists.txt</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fast.orig/source/FAST/Algorithms/NeuralNetwork/CMakeLists.txt 2019-08-11 08:27:52.570019237 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast/source/FAST/Algorithms/NeuralNetwork/CMakeLists.txt 2019-08-11 08:27:52.562019167 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -16,17 +16,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> fast_add_process_object(ClassificationToText ImageClassificationNetwork.hpp)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> fast_add_process_object(SegmentationNetwork SegmentationNetwork.hpp)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> fast_add_process_object(ImageToImageNetwork ImageToImageNetwork.hpp)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if(FAST_MODULE_Visualization)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fast_add_test_sources(</span></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;">- Tests.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ImageClassifierTests.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- VolumeTests.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- )</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if(FAST_MODULE_WholeSlideImaging)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fast_add_test_sources(WSITests.cpp)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fast_add_example(measureNeuralNetworkPerformance measureNeuralNetworkPerformance.cpp)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif()</span></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;">-endif()</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if(FAST_MODULE_Visualization)</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;">+# fast_add_test_sources(</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Tests.cpp</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# ImageClassifierTests.cpp</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# VolumeTests.cpp</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" 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="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# if(FAST_MODULE_WholeSlideImaging)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# fast_add_test_sources(WSITests.cpp)</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;">+# fast_add_example(measureNeuralNetworkPerformance measureNeuralNetworkPerformance.cpp)</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;">+# endif()</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif()</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> #fast_add_example(timingNetwork timingNetwork.cpp)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> #fast_add_example(imageClassification imageClassification.cpp)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #fast_add_example(leftVentricleSegmentation leftVentricleSegmentation.cpp)</span></pre>
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<a href="https://salsa.debian.org/med-team/fast/commit/681f4ceb47d258845cab0412a1478b19bb210278#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">fix_test.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_source_openigtlink.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">prevent_cmake_downloading.patch</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">remove_unneeded_installs.patch</span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">use_system_libs.patch</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">disable_test</span>s.patch</span></pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">set_cmake_option</span>s.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/fast/commit/681f4ceb47d258845cab0412a1478b19bb210278#7c7a56b25cab05d40c3313c0d8a70f58caf600b0"><strong>debian/patches/disable_tests.patch</strong>
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<strong>debian/patches/set_cmake_options.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: <span class="idiff left right">disable source's test suite</span></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> <span class="idiff left right">This is problematic and is currently disabled to not hinder productivity until this is figured out.</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: <span class="idiff left right">modify cmake options for build</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> <span class="idiff left right">Customise by setting some cmake options</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-08-08</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">Index: fast/CMakeLists.txt</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fast.orig/CMakeLists.txt 2019-08-10 18:21:35.603460183 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast/CMakeLists.txt 2019-08-10 18:22:07.003758309 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -15,10 +15,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> include(cmake/Macros.cmake)</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> #### Options</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-option(FAST_BUILD_TESTS "Build FAST tests." ON)</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;">+option(FAST_BUILD_TESTS "Build FAST tests." OFF)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fast.orig/CMakeLists.txt 2019-08-11 07:16:23.604778105 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast/CMakeLists.txt 2019-08-11 07:16:41.540933812 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> option(FAST_BUILD_TESTS "Build FAST tests." ON)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> option(FAST_BUILD_EXAMPLES "Build examples." OFF)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> option(FAST_BUILD_TOOLS "Build tools." ON)</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-option(FAST_BUILD_DOCS "Build API documentation" OFF)</span></span>
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