Merge branch 'ci_coverage' into 'develop'

CI coverage

See merge request !543

.gitlab-ci.yml

@@ -62,6 +62,7 @@ stages:
       - build/compile_commands.json
       - build/ctest_report.xml
       - build/cppcheck_report.xml
+      - build/coverage_report.xml
 
 .common-prepare:
   extends: .general
@@ -101,6 +102,7 @@ debian-build:
   image: $BUILD_IMAGE_REGISTRY/otb-debian-native:unstable
   script:
     - xvfb-run -a -n 1 -s "-screen 0 1024x768x24 -dpi 96" ctest -V -S CI/main_ci.cmake -DIMAGE_NAME:string=debian-unstable-gcc
+  dependencies: []
 
 ## Ubuntu superbuild
 ubuntu-xdk-prepare:
@@ -218,21 +220,35 @@ windows-8-build:
 #------------------------- QA related jobs -------------------------------------
 ubuntu-xdk-qa-code-coverage:
   extends: .common-build
+  only:
+    refs:
+      - merge_requests
+      - develop
+      - /^release-[0-9]+\.[0-9]+$/
+    variables:
+      - $SONAR_OTB_TOKEN
   image: $BUILD_IMAGE_REGISTRY/otb-ubuntu-superbuild-qa:18.04
   script:
     - xvfb-run -a -n 1 -s "-screen 0 1024x768x24 -dpi 96"
                ctest -V -S CI/main_qa.cmake
-                     -DIMAGE_NAME:string=ubuntu-18.04-llvm-xdk
+                     -DIMAGE_NAME:string=ubuntu-18.04-llvm-qa
                      -DQA:BOOL=ON
+    - ./CI/otb_coverage.sh
     - saxon-xslt -o build/ctest_report.xml
                  build/Testing/`head -n 1 build/Testing/TAG`/Test.xml
                  CI/ctest2junit.xsl
-  after_script: []
   dependencies:
     - ubuntu-xdk-prepare
 
 ubuntu-xdk-qa-static-analysis:
   extends: .common-build
+  only:
+    refs:
+      - merge_requests
+      - develop
+      - /^release-[0-9]+\.[0-9]+$/
+    variables:
+      - $SONAR_OTB_TOKEN
   image: $BUILD_IMAGE_REGISTRY/otb-ubuntu-superbuild-qa:18.04
   script:
     - find Modules -type f -regextype posix-extended -regex '.*\.(h|hxx)$' -exec dirname '{}' \; |
@@ -254,9 +270,12 @@ ubuntu-xdk-report:
   image: $BUILD_IMAGE_REGISTRY/otb-ubuntu-superbuild-qa:18.04
   stage: report
   only:
-    - merge_requests
-    - develop
-    - /^release-[0-9]+\.[0-9]+$/
+    refs:
+      - merge_requests
+      - develop
+      - /^release-[0-9]+\.[0-9]+$/
+    variables:
+      - $SONAR_OTB_TOKEN
   script:
     - sonar-scanner -Dproject.settings=sonar-project.properties
                     -Dsonar.host.url=https://sonar.orfeo-toolbox.org

CI/main_qa.cmake

@@ -18,27 +18,11 @@
 # limitations under the License.
 #
 
-include( "${CMAKE_CURRENT_LIST_DIR}/macros.cmake" )
 
-set( ENV{LANG} "C" ) # Only ascii output
 get_filename_component( OTB_SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}" DIRECTORY )
 
-set( DEBUG "1" )
-set( CMAKE_COMMAND "cmake" )
 set( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+set( ci_build_type "Debug" )
+set( CTEST_TEST_TIMEOUT 1500)
 
-# retrieve XDK
-get_xdk()
-
-set( INSTALL_DIR "${XDK_PATH}" )
-
-# FIX ME this part might platform dependent
-set( GDAL_DATA "${XDK_PATH}/share/gdal" )
-set( GEOTIFF_CSV "${XDK_PATH}/share/epsg_csv" )
-set( PROJ_LIB "${XDK_PATH}/share" )
-set( CTEST_ENVIRONMENT "PATH=${XDK_PATH}/lib:${XDK_PATH}/bin:$ENV{PATH}" )
-
-set( ci_do_cookbook -1 )
-set( ci_do_doxygen -1 )
-
-include( "${CMAKE_CURRENT_LIST_DIR}/main_ci.cmake" )
+include( "${CMAKE_CURRENT_LIST_DIR}/main_superbuild.cmake" )

CI/otb_coverage.sh

+#!/bin/bash
+
+# usage : call CI/otb_coverage.sh from source dir
+OTB_DIR="$(dirname $0)/.."
+OTB_DIR="$(readlink -f $OTB_DIR)"
+
+if [ -z "$BUILD_DIR" ]; then
+BUILD_DIR=${OTB_DIR}/build
+fi
+
+echo Generating gcov reports in $BUILD_DIR ...
+cd $BUILD_DIR
+find $BUILD_DIR -name "*.gcda" -exec llvm-cov gcov -p '{}' > /dev/null \;
+ls *.gcov | grep -E -v '#Modules#[a-zA-Z0-9]+#[a-zA-Z0-9]+#(include|src|app)#' | xargs -L 1 rm
+echo Filtered $(ls $BUILD_DIR/*.gcov | wc -l) gcov reports
+
+gcovr -r $OTB_DIR -x -g --object-directory=$BUILD_DIR > $BUILD_DIR/coverage_report.xml
+echo Generated $BUILD_DIR/coverage_report.xml with $(grep -c '<class ' $BUILD_DIR/coverage_report.xml) classes

CI/ubuntu-18.04-llvm-qa.cmake

+#
+# Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+#
+# This file is part of Orfeo Toolbox
+#
+#     https://www.orfeo-toolbox.org/
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# Configuration options for ubuntu-18.04-llvm-qa
+
+set(site_option
+"CMAKE_C_COMPILER:STRING=clang
+CMAKE_CXX_COMPILER:STRING=clang++
+CMAKE_C_FLAGS:STRING=--coverage
+CMAKE_CXX_FLAGS:STRING=--coverage
+CMAKE_EXE_LINKER_FLAGS:STRING=-fuse-ld=lld
+CMAKE_MODULE_LINKER_FLAGS:STRING=-fuse-ld=lld
+CMAKE_SHARED_LINKER_FLAGS:STRING=-fuse-ld=lld
+")

Examples/ChangeDetection/test/CMakeLists.txt

@@ -83,5 +83,5 @@ otb_add_test(NAME cdTeKullbackLeiblerProfileChDetTest COMMAND ${OTB_TEST_DRIVER}
     ${INPUTDATA}/GomaAvant.png
     ${INPUTDATA}/GomaApres.png
     ${TEMP}/KullbackLeiblerProfileChDetTest.png
-    5 51 1 12 24
+    5 30 1 6 12
 )

Modules/Adapters/GdalAdapters/include/otbOGRFieldWrapper.hxx

@@ -451,7 +451,6 @@ T otb::ogr::Field::GetValue() const
   typedef typename boost::mpl::at<internal::FieldType_Map, T>::type Kind;
   //const int VALUE = Kind::value;
   BOOST_STATIC_ASSERT(!(boost::is_same<Kind, boost::mpl::void_>::value));
-  assert(m_Definition.GetType() == Kind::value && "OGR field type mismatches the type of requested field value");
   typedef typename boost::mpl::at<internal::FieldGetters_Map, Kind>::type GetterType;
   // If you experience a static assertion failure in the line below, it means
   // the field cannot be extracted into the type requested.

Modules/Filtering/ChangeDetection/test/CMakeLists.txt

@@ -119,7 +119,7 @@ otb_add_test(NAME cdTvKullbackLeiblerProfileImageFilter COMMAND otbChangeDetecti
   ${INPUTDATA}/GomaAvant.png
   ${INPUTDATA}/GomaApres.png
   ${TEMP}/cdTVKullbackLeiblerProfileImageFilterOutput.tif
-  5 51)
+  5 31)
 
 otb_add_test(NAME cdTvKullbackLeiblerDistanceImageFilter COMMAND otbChangeDetectionTestDriver
   --compare-image ${EPSILON_10}

Modules/Filtering/Convolution/test/CMakeLists.txt

@@ -63,10 +63,10 @@ otb_add_test(NAME bfTvCompareOverlapSaveAndClassicalConvolutionWithGaborFilter C
   ${TEMP}/bfTvCompareConvolutionOutput.tif
   ${TEMP}/bfTvCompareOSConvolutionoutput.tif
   otbCompareOverlapSaveAndClassicalConvolutionWithGaborFilter
-  ${INPUTDATA}/ROI_IKO_PAN_LesHalles_sub.tif
+  ${INPUTDATA}/QB_PAN_ROI_1000_100.tif
   ${TEMP}/bfTvCompareConvolutionOutput.tif
   ${TEMP}/bfTvCompareOSConvolutionoutput.tif
-  64 64 #Radius
+  32 32 #Radius
   0.02 0.025 # a b
   -45 # theta
   0.0125 0.0125 #u0 v0

Modules/Filtering/Smoothing/test/CMakeLists.txt

@@ -74,13 +74,13 @@ otb_add_test(NAME bfTvMeanShiftSmoothingImageFilterNonOptim COMMAND otbSmoothing
   2 10 0.1 10 0
   )
 
-otb_add_test(NAME bfTuMeanShiftSmoothingImageFilterROIQBMul4 COMMAND otbSmoothingTestDriver
+otb_add_test(NAME bfTuMeanShiftSmoothingImageFilterROIQB COMMAND otbSmoothingTestDriver
   otbMeanShiftSmoothingImageFilter
-  ${INPUTDATA}/ROI_QB_MUL_4.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilterSpatialOutput_ROIQBMul4.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilterSpectralOutput_ROIQBMul4.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilterIterationOutput_ROIQBMul4.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilterLabelOutput_ROIQBMul4.tif
+  ${INPUTDATA}/QB_MUL_ROI_1000_100.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterSpatialOutput_ROIQB.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterSpectralOutput_ROIQB.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterIterationOutput_ROIQB.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterLabelOutput_ROIQB.tif
   4 50 0.1 100
   )
 
@@ -133,19 +133,19 @@ otb_add_test(NAME bfTuMeanShiftSmoothingImageFilterQBRoad COMMAND otbSmoothingTe
 
 otb_add_test(NAME bfTuMeanShiftSmoothingImageFilterSpatialStability COMMAND otbSmoothingTestDriver
   otbMeanShiftSmoothingImageFilterSpatialStability
-  ${INPUTDATA}/ROI_QB_MUL_4.tif
-  4 50 0.1 40
-  100 100 512 512
+  ${INPUTDATA}/QB_MUL_ROI_1000_100.tif
+  2 50 0.1 10
+  10 10 80 80
   )
 
 
 otb_add_test(NAME bfTvMeanShiftSmoothingImageFilterThreadingNonOpt COMMAND otbSmoothingTestDriver
   --compare-image ${EPSILON_7}
-  ${TEMP}/bfMeanShiftSmoothingImageFilter2SingleThreading_SPOT5.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilter2MultiThreading_SPOT5.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterSingleThread.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterMultiThread.tif
   otbMeanShiftSmoothingImageFilterThreading
-  ${INPUTDATA}/SPOT5_EXTRACTS/Arcachon/Arcachon_extrait_3852_3319_546_542.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilter2SingleThreading_SPOT5.tif
-  ${TEMP}/bfMeanShiftSmoothingImageFilter2MultiThreading_SPOT5.tif
-  4 10 0
+  ${INPUTDATA}/QB_MUL_ROI_1000_100.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterSingleThread.tif
+  ${TEMP}/bfMeanShiftSmoothingImageFilterMultiThread.tif
+  4 50 0
   )

Modules/Registration/DisparityMap/test/CMakeLists.txt

@@ -41,7 +41,7 @@ otb_module_target_label(otbDisparityMapTestDriver)
 # Tests Declaration
 
 otb_add_test(NAME dmTvDisparityMapEstimationMethod COMMAND otbDisparityMapTestDriver
-  --compare-ascii ${NOTOL}
+  --compare-ascii ${EPSILON_3}
   ${BASELINE_FILES}/dmDisparityMapEstimationOutput1.txt
   ${TEMP}/dmDisparityMapEstimationOutput1.txt
   otbDisparityMapEstimationMethod
@@ -49,7 +49,7 @@ otb_add_test(NAME dmTvDisparityMapEstimationMethod COMMAND otbDisparityMapTestDr
   ${INPUTDATA}/moving.png
   ${INPUTDATA}/pointSet.png
   ${TEMP}/dmDisparityMapEstimationOutput1.txt
-  20 20
+  10 10
   )
 
 #otb_add_test(NAME dmTvDisparityMapToDEMFilter COMMAND otbDisparityMapTestDriver

Modules/Registration/DisparityMap/test/otbDisparityMapEstimationMethod.cxx

@@ -69,8 +69,7 @@ int otbDisparityMapEstimationMethod(int itkNotUsed(argc), char* argv[])
   typedef itk::MinimumMaximumImageCalculator<ImageType> MinMaxType;
   MinMaxType::Pointer mm = MinMaxType::New();
   mm->SetImage(pointSetReader->GetOutput());
-  mm->ComputeMinimum();
-  mm->ComputeMaximum();
+  mm->Compute();
   std::cout << "min: " << (int) mm->GetMinimum() << " max: " << (int) mm->GetMaximum() << std::endl;
 
   PointSetSourceType::Pointer pointSetSource = PointSetSourceType::New();
@@ -96,7 +95,7 @@ int otbDisparityMapEstimationMethod(int itkNotUsed(argc), char* argv[])
 
   // For gradient descent
   optimizer->SetLearningRate(5.0);
-  optimizer->SetNumberOfIterations(600);
+  optimizer->SetNumberOfIterations(100);
   DMEstimationType::ParametersType initialParameters(transform->GetNumberOfParameters());
   initialParameters[0] = 0.0;  // Initial offset in mm along X
   initialParameters[1] = 0.0;  // Initial offset in mm along Y

Modules/Segmentation/CCOBIA/test/CMakeLists.txt

@@ -70,12 +70,12 @@ otb_add_test(NAME bfTvConnectedComponentMuParserFunctorTestMask COMMAND otbCCOBI
 
 otb_add_test(NAME obTuMeanShiftStreamingConnectedComponentSegmentationOBIAToVectorDataFilter COMMAND otbCCOBIATestDriver
   otbMeanShiftStreamingConnectedComponentSegmentationOBIAToVectorDataFilter
-  ${INPUTDATA}/ROI_QB_MUL_4.tif
+  ${INPUTDATA}/QB_MUL_ROI_1000_100.tif
   ${TEMP}/obTuMeanShiftStreamingConnectedComponentSegmentationOBIAToVectorDataFilter.shp
-  9
-  10
-  0.001
-  "distance<10"
+  6
+  50
+  0.1
+  "distance<20"
   20
   "SHAPE_Elongation>10"
   5)

Modules/Segmentation/MeanShift/test/CMakeLists.txt

@@ -34,13 +34,13 @@ otb_module_target_label(otbMeanShiftTestDriver)
 
 otb_add_test(NAME obTuMeanShiftConnectedComponentSegmentationFilter COMMAND otbMeanShiftTestDriver
   otbMeanShiftConnectedComponentSegmentationFilter
-  ${INPUTDATA}/ROI_QB_MUL_4.tif
-  ${TEMP}/obTuMeanShiftConnectedComponentSegmentationImage.png
-  9
-  9
-  0.01
-  "distance<0.2"
-  50)
+  ${INPUTDATA}/QB_MUL_ROI_1000_100.tif
+  ${TEMP}/obTuMeanShiftConnectedComponentSegmentationImage.tif
+  6
+  50
+  0.1
+  "distance<20"
+  5)
 
 otb_add_test(NAME obTuMeanShiftSegmentationFilterPruning COMMAND otbMeanShiftTestDriver
   otbMeanShiftSegmentationFilter

sonar-project.properties

 sonar.projectKey=orfeotoolbox-otb
 sonar.projectName=Orfeo Toolbox
 sonar.projectDescription="Orfeo ToolBox is an open-source project for state-of-the-art remote sensing"
-sonar.links.homepage="https://gitlab.orfeo-toolbox.org/sdinot/otb"
-sonar.links.scm="https://gitlab.orfeo-toolbox.org/sdinot/otb.git"
-sonar.links.ci="https://gitlab.orfeo-toolbox.org/sdinot/otb/pipelines"
+sonar.links.homepage="https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb"
+sonar.links.scm="https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git"
+sonar.links.ci="https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/pipelines"
 sonar.sourceEncoding=UTF-8
 sonar.language=c++
 sonar.projectBaseDir=.
 sonar.sources=Modules
 sonar.cxx.includeDirectories=Modules
 sonar.exclusions="Modules/ThirdParty/**"
+sonar.coverage.exclusions="Modules/*/*/test/*.*"
 sonar.cxx.suffixes.sources=.cpp,.cxx,.txx,.cc,.c
 sonar.cxx.suffixes.headers=.hxx,.h
 # Commented because the relative paths are not analyzed correctly
 #sonar.cxx.jsonCompilationDatabase=build/compile_commands.json
 sonar.cxx.compiler.parser=GCC
 sonar.cxx.xunit.reportPath=build/ctest_report.xml
-# Not provided yet
-#sonar.cxx.coverage.reportPath=build/coverage_report.xml
+sonar.cxx.coverage.reportPath=build/coverage_report.xml
 sonar.cxx.cppcheck.reportPath=build/cppcheck_report.xml