Added files for CMake, CI and coverage

.gitignore

@@ -37,3 +37,4 @@
 bin
 obj
 lib
+build

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "UnitTest-cpp"]
+	path = UnitTest-cpp
+	url = https://github.com/liyier90/UnitTest-cpp

.travis.yml

@@ -0,0 +1,36 @@
+language: cpp
+
+os: linux
+dist: bionic
+compiler: gcc
+sudo: true
+matrix:
+  include:
+    - env: BUILD=Debug COVERAGE=OFF
+    - env: BUILD=Release COVERAGE=OFF
+    - env: BUILD=Debug COVERAGE=ON
+
+before_script:
+  - sudo apt-get install -yq lcov
+
+script:
+  - git submodule update --init --recursive
+  - cd UnitTest-cpp
+  - mkdir -p lib/${BUILD}
+  - cd lib/${BUILD}
+  - cmake ../.. -DCMAKE_BUILD_TYPE=${BUILD}
+  - make
+  - cd ../../..
+  - mkdir -p build
+  - cd build
+  - cmake .. -DCMAKE_BUILD_TYPE=${BUILD} -DUnfit_ENABLE_TESTING=ON -DUnfit_COVERAGE=${COVERAGE}
+  - make
+  - if [ $COVERAGE == "ON" ];
+    then make coverage;
+    else ./UnfitTest;
+    fi
+
+after_success:
+  - if [ $COVERAGE == "ON" ]; then
+    bash <(curl -s https://codecov.io/bash) -f coverage.info.cleaned -t "30ccfca2-015e-4c4e-913f-3cae31ea6673" || echo "Codecov did not collect coverage reports";
+    fi

CMakeLists.txt

@@ -0,0 +1,114 @@
+cmake_minimum_required(VERSION 3.10)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
+include(EnsureOutOfSourceBuild)
+ensure_out_of_source_build()
+project(Unfit)
+
+#######################################################################
+# Set up compiler and build type
+#######################################################################
+include(UnfitCompilerFlags)
+option(Unfit_ENABLE_TESTING "Enable Unfit Testing" OFF)
+option(Unfit_COVERAGE "Build Unfit with coverage information" OFF)
+
+if(Unfit_COVERAGE)
+  set(Unfit_ENABLE_TESTING ON)
+  set(CMAKE_BUILD_TYPE "Debug")
+endif()
+
+#######################################################################
+# Find libraries
+#######################################################################
+set(Unfit_INCLUDES include examples)
+set(Unfit_LINK_LIBRARIES "")
+
+# Check prereqs
+if(Unfit_COVERAGE)
+  find_program(GCOV_PATH gcov)
+  find_program(LCOV_PATH lcov)
+  find_program(GENHTML_PATH genhtml)
+  find_program(GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/unittests)
+
+  if(NOT GCOV_PATH)
+    message(FATAL_ERROR "gcov not found! Aborting...")
+  endif()
+
+  if(NOT LCOV_PATH)
+    message(FATAL_ERROR "lcov not found! Aborting...")
+  endif()
+
+  if(NOT GENHTML_PATH)
+    message(FATAL_ERROR "genhtml not found! Aborting...")
+  endif()
+endif()
+
+if(Unfit_ENABLE_TESTING)
+  list(APPEND Unfit_INCLUDES
+      "${Unfit_SOURCE_DIR}/UnitTest-cpp"
+      "${Unfit_SOURCE_DIR}/UnitTest-cpp/UnitTest++/src")
+  if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+    list(APPEND Unfit_LINK_LIBRARIES
+        "${Unfit_SOURCE_DIR}/UnitTest-cpp/lib/Debug/libUnitTest++.a")
+  else()
+    list(APPEND Unfit_LINK_LIBRARIES
+        "${Unfit_SOURCE_DIR}/UnitTest-cpp/lib/Release/libUnitTest++.a")
+  endif()
+endif()
+
+#######################################################################
+# Find pthread
+#######################################################################
+set(THREADS_PREFER_PTHREAD_FLAG_ON)
+find_package(Threads REQUIRED)
+list(APPEND Unfit_LINK_LIBRARIES Threads::Threads)
+
+#######################################################################
+# Configure build
+#######################################################################
+file(GLOB SOURCES "src/*.cpp")
+if(Unfit_ENABLE_TESTING)
+  file(GLOB TEST_SOURCES "examples/*.cpp" "unittests/*.cpp")
+  file(COPY "${Unfit_SOURCE_DIR}/examples/data"
+      DESTINATION "${Unfit_BINARY_DIR}/examples")
+  file(COPY "${Unfit_SOURCE_DIR}/unittests/data"
+      DESTINATION "${Unfit_BINARY_DIR}/unittests")
+
+  set(target_name ${PROJECT_NAME}Test)
+  list(FILTER SOURCES EXCLUDE REGEX "main.cpp$")
+  add_executable(${target_name} ${SOURCES} ${TEST_SOURCES})
+  target_include_directories(${target_name} PUBLIC ${Unfit_INCLUDES})
+  target_link_libraries(${target_name} ${Unfit_LINK_LIBRARIES})
+else()
+  set(target_name ${PROJECT_NAME}Example)
+  list(FILTER SOURCES EXCLUDE REGEX ".*-test.cpp$")
+  add_executable(${target_name} ${SOURCES} "examples/ParabolicModel.hpp")
+  target_include_directories(${target_name} PUBLIC include PUBLIC examples)
+  target_link_libraries(${target_name} ${Unfit_LINK_LIBRARIES})
+endif()
+
+if(Unfit_COVERAGE)
+  # Run test with low priority (+15)
+  set(NICE_COMMAND nice)
+  set(NICENESS -15)
+  set(_output_name coverage)
+  add_custom_target(coverage
+      # Cleanup lcov
+      ${LCOV_PATH} --directory . --zerocounters
+
+      # Run tests
+      COMMAND ${NICE_COMMAND} ${NICENESS} "./${target_name}"
+
+      # Capture lcov counters
+      COMMAND ${LCOV_PATH} --directory . --capture --output-file ${_output_name}.info
+      COMMAND ${LCOV_PATH} --remove ${_output_name}.info /usr/* */UnitTest-cpp/* */unittests/* */examples/Test*.cpp --output-file ${_output_name}.info.cleaned
+      set(_page_title "\"Unfit Coverage Results\"")
+      COMMAND ${GENHTML_PATH} --title "${_page_title}" --no-function-coverage -o ${_output_name} ${_output_name}.info.cleaned
+      COMMAND ${CMAKE_COMMAND} -E remove ${_output_name}.info
+      COMMAND ${LCOV_PATH} --list ${_output_name}.info.cleaned
+
+      WORKING_DIRECTORY ${Chaste_BINARY_DIR}
+      COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+      VERBATIM)
+endif()

README.md

@@ -1,4 +1,7 @@
-# Unfit
+Unfit<br>
+[![Build Status](https://travis-ci.org/liyier90/Unfit.svg?branch=master)](https://travis-ci.org/liyier90/Unfit)
+[![codecov](https://codecov.io/gh/liyier90/Unfit/branch/master/graph/badge.svg)](https://codecov.io/gh/liyier90/Unfit)
+==========
 Data fitting and optimization software
 
 ### Getting Started (User Version)

cmake/Modules/EnsureOutOfSourceBuild.cmake

@@ -0,0 +1,20 @@
+macro(ensure_out_of_source_build)
+  get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
+  get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
+
+  if("${srcdir}" STREQUAL "${bindir}")
+    message("****************************************************************")
+    message("* Please build outside the source directory. For example:      *")
+    message("*   mkdir ~/tmp/build")
+    message("*   cd ~/tmp/build")
+    message("*   cmake ${CMAKE_SOURCE_DIR}")
+    message("*                                                              *")
+    message("* Please remove the following files:")
+    message("*   ${CMAKE_SOURCE_DIR}/CMakeCache.txt")
+    message("*   ${CMAKE_SOURCE_DIR}/CMakeFiles/*")
+    message("*                                                              *")
+    message("* before the next configuration attempt to avoid this message. *")
+    message("****************************************************************")
+    message(FATAL_ERROR "Quitting configuration")
+  endif()
+endmacro(ensure_out_of_source_build)

cmake/Modules/UnfitCompilerFlags.cmake

@@ -0,0 +1,17 @@
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -std=c++11")
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+endif()
+if(CMAKE_BUILD_TYPE STREQUAL "Release")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -s")
+endif()
+
+if(Unfit_COVERAGE)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+endif()
+
+string(CONCAT CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Weffc++ -Wextra "
+    "-pedantic -Winit-self -Wmissing-declarations -Wmissing-include-dirs "
+    "-Wundef -Wredundant-decls -Wfloat-equal -Wmain -Wunreachable-code "
+    "-Wshadow -Wcast-align -Wswitch-enum")