CI improvements

Former-commit-id: bb6087f6

.gitlab-ci.yml

@@ -5,24 +5,27 @@ stages:
 
 unit_tests:
   stage: unit_tests
-  variables:
-    CTEST_OUTPUT_ON_FAILURE: "TRUE"
   script:
     - git submodule update --init --recursive
     - cd code/build/release
-    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ../../
+    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug ../../
     - ninja
-    - ninja test
-  timeout: 2h
-  only:
-    refs:
-      - develop
-      - master
-      - merge_requests
-    changes:
-      - "code/include/**/*"
-      - "code/tests/**/*"
-      - "code/src/**/*"
-      - "code/CMakeLists.txt"
-      - "scripts/Dockerfile"
-      - ".gitmodules"
+    - OMP_NUM_THREADS=1 ./unit_tests -r junit > unit_tests_report.xml
+    - gcovr -e ../../ext/ -e ../../tests/ -r ../../
+  artifacts:
+    when: always
+    paths:
+      - code/build/release/unit_tests_report.xml
+    reports:
+      junit: code/build/release/unit_tests_report.xml
+  timeout: 4h
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "develop"
+      changes:
+        - "code/include/**/*"
+        - "code/tests/**/*"
+        - "code/src/**/*"
+        - "code/CMakeLists.txt"
+        - "scripts/Dockerfile"
+        - ".gitmodules"
+    - if: $CI_PIPELINE_SOURCE == "web"

README.md

+[![pipeline status](https://git.scc.kit.edu/rtsn/rtsn/badges/master/pipeline.svg)](https://git.scc.kit.edu/rtsn/rtsn/-/commits/master) [![coverage report](https://git.scc.kit.edu/rtsn/rtsn/badges/master/coverage.svg)](https://git.scc.kit.edu/rtsn/rtsn/-/commits/master)
+
 # KiT-RT - an HPC Radio Therapy $`S_n`$ framework
 TBD 
 ## What KiT-RT is capable of
@@ -52,17 +54,17 @@ The resulting executable will automatically be placed in the `code/bin` folder.
 
 ## Run
 ### Local
-Execute the compiled binary and hand over a valid *TOML*-styled config file.
+Execute the compiled binary from the `bin` folder and hand over a valid *TOML*-styled config file.
 Example from inside the `code` directory:
 
 ```bash
-./bin/KiT-RT input/example.cfg
+./KiT-RT ../input/example.cfg
 ```
 
 In order to run the code in parallel execute:
 
 ```bash
-OMP_NUM_THREADS=N mpirun -np J ./bin/KiT-RT input/example.cfg
+OMP_NUM_THREADS=N mpirun -np J ./KiT-RT ../input/example.cfg
 ```
 
 with `N` equal to the number of shared memory threads and `J` equal to the number of distrubuted memory threads.

code/CMakeLists.txt

@@ -12,6 +12,8 @@ set( KITRT_DEBUG_OPTIONS -Wall -Wextra -Wpedantic )
 
 
 ### LIBRARIES ###################################
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
 find_package( OpenMP REQUIRED )
 
 find_package( MPI REQUIRED )
@@ -38,7 +40,7 @@ else()
     message( STATUS "Blaze: BLAS mode disabled" )
     add_compile_definitions( BLAZE_BLAS_MODE=0 )
 endif()
-include( ${CMAKE_SOURCE_DIR}/cmake/blaze-cache-config.cmake )
+include( blaze-cache-config )
 include_directories( ${CMAKE_SOURCE_DIR}/ext/blaze )
 
 add_compile_definitions( METIS_EXPORT= )
@@ -81,6 +83,7 @@ target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:RELEASE>:${KITR
 ### BUILD UNIT TESTS ############################
 include( CTest )
 set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
+add_compile_definitions( BUILD_TESTING )
 add_compile_definitions( TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
 add_library( Catch INTERFACE )
 target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
@@ -89,6 +92,11 @@ list( REMOVE_ITEM SRCS "src/main.cpp" )
 add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
 target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
 target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+if( CMAKE_COMPILER_IS_GNUCXX )
+    set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
+    target_link_libraries( unit_tests Catch gcov )
+endif()
 target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
 target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
 add_test( NAME unit_tests COMMAND unit_tests )

scripts/Dockerfile

 FROM ubuntu:20.04
 
-ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib" \
+    PYTHONPATH=/usr/local/gmsh/lib:$PYTHONPATH \
+    PATH=/usr/local/gmsh/bin:$PATH 
 
 RUN apt-get update \
     && DEBIAN_FRONTEND=noninteractive apt-get install -qq \
@@ -19,14 +21,24 @@ RUN apt-get update \
        libssl-dev \
        libxt-dev \
        libgl1-mesa-dev \
+       libglu1 \
+       libxrender1 \
+       libxcursor-dev \
+       libxft-dev \
+       libxinerama-dev \
        python3 \
        python3-pip \
-       gmsh \
     && apt-get clean \
     && apt-get autoremove --purge \
     && rm -rf /var/lib/apt/lists/* 
 
-RUN wget --no-check-certificate --quiet https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz \
+RUN cd /usr/local \
+    && wget -nc --quiet  http://gmsh.info/bin/Linux/gmsh-4.7.0-Linux64-sdk.tgz \
+    && tar xzf gmsh-4.7.0-Linux64-sdk.tgz \
+    && mv gmsh-4.7.0-Linux64-sdk gmsh \
+    && rm gmsh-4.7.0-Linux64-sdk.tgz 
+
+RUN wget -nc --no-check-certificate --quiet https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz \
     && tar xzf VTK-8.2.0.tar.gz \
     && mkdir VTK-8.2.0/build \
     && cd VTK-8.2.0/build \
@@ -36,6 +48,6 @@ RUN wget --no-check-certificate --quiet https://www.vtk.org/files/release/8.2/VT
     && cd - \
     && rm -rf VTK-*
 
-RUN pip3 install numpy pygmsh Pillow pydicom
+RUN pip3 install numpy pygmsh==6.1.1 Pillow pydicom gcovr
 
 WORKDIR /home