Merge pull request #29 from jpatton-USGS/updates

Updates for Machine Learning applications - requested changes incorporated

.travis.yml

@@ -14,6 +14,12 @@ addons:
       - libgtest-dev
       - lcov
       - cppcheck
+      - doxygen
+      - doxygen-doc
+      - doxygen-latex
+      - doxygen-gui
+      - graphviz
+      - unzip
     sources:
       - ubuntu-toolchain-r-test
 
@@ -59,14 +65,15 @@ before_script:
     - g++-5 --version 2>&1 | grep g++-5
 
 script:
-  # Java build, tests, and coverage
+  # Java build, tests, javadocs, and coverage
   - cd ${TRAVIS_BUILD_DIR}/java
-  - ant coverage
+  - ant all
   # C++ build, tests, and coverage
   - cd ${TRAVIS_BUILD_DIR}/cpp
   - mkdir build
+  - mkdir dist
   - cd build
-  - cmake -DRUN_TESTS=1 -DSUPPORT_COVERAGE=1 -DRUN_COVERAGE=1 -DRUN_CPPCHECK=1 -DRAPIDJSON_PATH=../lib/rapidjson .. && make
+  - cmake -DRUN_TESTS=1 -DSUPPORT_COVERAGE=1 -DRUN_COVERAGE=1 -DRUN_CPPCHECK=1 -DRUN_CPPLINT=1 -DGENERATE_DOCUMENTATION=1 -DCMAKE_INSTALL_PREFIX=../dist -DRAPIDJSON_PATH=../../lib/rapidjson -DCPPLINT_PATH=../../lib/cpplint/cpplint.py -DCPPCHECK_PATH=/usr/bin/cppcheck .. && make
   # python tests
   - cd ${TRAVIS_BUILD_DIR}/python
   - python -m unittest discover test/

.vscode/c_cpp_properties.json

@@ -0,0 +1,20 @@
+{
+    "configurations": [
+        {
+            "name": "Mac",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${workspaceFolder}/lib/rapidjson/*",
+                "${workspaceFolder}/cpp/include/*"
+            ],
+            "defines": [],
+            "macFrameworkPath": [
+                "/System/Library/Frameworks",
+                "/Library/Frameworks"
+            ],
+            "compilerPath": "/usr/bin/clang",
+            "intelliSenseMode": "clang-x64"
+        }
+    ],
+    "version": 4
+}

codecov.yml

@@ -1,3 +1,3 @@
 ignore:
   - "cpp/tests"  # ignore tests
-  - "cpp/lib"    # ignore external libraries
+  - "lib"    # ignore external libraries

cpp/CMakeLists.txt

@@ -1,278 +1,66 @@
+# earthquake-detection-formats CMake configuration file.
 cmake_minimum_required (VERSION 3.4)
+set(CMAKE_DIR ${CMAKE_CURRENT_LIST_DIR}/cmake/)
 
-# ----- VERSION NUMBER----- #
-set(VERSION_MAJOR 0)
-set(VERSION_MINOR 9)
-set(VERSION_PATCH 0)
+# ----- PROJECT VERSION ----- #
+include(${CMAKE_DIR}/version.cmake)
 
 # ----- PROJECT ----- #
-project (DetectionFormats VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
+project (DetectionFormats VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
 
-include(internal_utils.cmake)
+#----- BASE FUNCTIONS ----- #
+include(${CMAKE_DIR}/base.cmake)
 
-fix_default_compiler_settings()  # Defined in internal_utils.cmake.
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif(NOT CMAKE_BUILD_TYPE)
 
-# ----- NON WINDOWS CONFIG ----- #
-if (NOT MSVC)
-    # C++ 14 Standard
-    SET(GCC_CXX_14_FLAGS "-std=c++14")
-    SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} ${GCC_CXX_14_FLAGS} ")
+# ----- CMAKE INCLUDES ----- #
+include(ExternalProject)
 
-    option(SUPPORT_COVERAGE "Instrument for Coverage" OFF)
+# ----- SETUP INSTALL LOCATIONS ----- #
+set(INSTALL_LOCATION ${CMAKE_INSTALL_PREFIX})
 
-    if(SUPPORT_COVERAGE)
-        # Coverage
-        SET(GCC_COVERAGE_COMPILE_FLAGS "-fprofile-arcs -ftest-coverage")
-        SET(GCC_COVERAGE_LINK_FLAGS "--coverage")
+# ----- PREPEND INSTALL LOCATIONS TO MODULE PATH ----- #
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${INSTALL_LOCATION}" )
 
-        # set flags
-        SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} ${GCC_CXX_14_FLAGS} ${GCC_COVERAGE_COMPILE_FLAGS}")
-        SET(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} ${GCC_COVERAGE_LINK_FLAGS}")
-    endif (SUPPORT_COVERAGE)
-endif (NOT MSVC)
-
-# ----- CMAKE CONFIG HEADER ----- #
-# pass some of the CMake settings
-# to the source code
-configure_file (
-    "${PROJECT_SOURCE_DIR}/DetectionFormatsCMakeConfig.h.in"
-    "${PROJECT_BINARY_DIR}/DetectionFormatsCMakeConfig.h"
-)
+# ----- OPTIONS ----- #
+option(GENERATE_DOCUMENTATION "Create and install the HTML based API documentation" OFF)
+option(RUN_TESTS "Create and run unit tests" ON)
+option(RUN_CPPCHECK "Run CPP Checks (requires cppcheck installed)" OFF)
+option(RUN_CPPLINT "Run CPP Checks (requires cpplint and python installed)" OFF)
+option(SUPPORT_COVERAGE "Instrument for Coverage" OFF)
+option(RUN_COVERAGE "Run Coverage Report (requires lcov installed)" OFF)
+option(GIT_CLONE_PUBLIC "Clone from public git URLs (https)" OFF)
 
 # ----- EXTERNAL LIBRARIES ----- #
 # rapidjson
-set(RAPIDJSON_PATH "${CURRENT_SOURCE_DIR}/lib/rapidjson" CACHE PATH "Path to rapidjson")
-
-# ----- SET INCLUDE DIRECTORIES ----- #
-include_directories(${PROJECT_BINARY_DIR})
-include_directories(${PROJECT_SOURCE_DIR}/include)
-include_directories(${RAPIDJSON_PATH}/..)
-include_directories(${RAPIDJSON_PATH})
+include(${CMAKE_DIR}/include_rapidjson.cmake)
 
 # ----- SET SOURCE FILES ----- #
 file(GLOB SRCS ${PROJECT_SOURCE_DIR}/src/*.cpp)
 
 # ----- SET HEADER FILES ----- #
 file(GLOB HDRS ${PROJECT_SOURCE_DIR}/include/*.h)
 
-# ----- CREATE LIBRARY ----- #
-add_library (DetectionFormats STATIC ${SRCS} ${HDRS})
-
-# ----- TARGET PROPERTIES ----- #
-set_target_properties(DetectionFormats PROPERTIES
-    OUTPUT_NAME DetectionFormats)
-
-# ----- GENERATE ----- #
-include(GenerateExportHeader)
-generate_export_header(DetectionFormats EXPORT_FILE_NAME ${CMAKE_CURRENT_BINARY_DIR}/DetectionFormats_export.h)
-
-# ----- GLOBAL INCLUDES ----- #
-target_include_directories(
-    DetectionFormats PUBLIC
-    "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}>"
-    "$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>"
-)
-
-# ----- TESTS ----- #
-option(RUN_TESTS "Create and run unit tests (requires GTest)" OFF)
-
-if (RUN_TESTS)
-
-    # ----- LOOK FOR GTEST ----- #
-    set(GTEST_ROOT "./" CACHE PATH "Path to the google test library")
-    find_package(GTest REQUIRED)
-
-    enable_testing()
-
-    # ----- TEST SOURCES ----- #
-    file(GLOB UNITTEST_SOURCES ${PROJECT_SOURCE_DIR}/tests/*.cpp)
-
-    if (NOT MSVC)
-        set(PTHREADLIB -pthread)
-    endif (NOT MSVC)
-
-    # ----- SET TEST INCLUDE DIRECTORIES ----- #
-    include_directories(${GTEST_INCLUDE_DIRS})
-
-    # ----- CREATE TEST EXE ----- #
-    add_executable(DetectionFormatsTests ${UNITTEST_SOURCES})
-    set_target_properties(DetectionFormatsTests PROPERTIES OUTPUT_NAME DetectionFormats-tests)
-    target_link_libraries(DetectionFormatsTests ${PTHREADLIB} ${GCC_COVERAGE_LINK_FLAGS} ${GTEST_BOTH_LIBRARIES})
-    target_link_libraries(DetectionFormatsTests DetectionFormats)
-
-    # ----- TESTS ----- #
-    GTEST_ADD_TESTS(DetectionFormatsTests "" ${UNITTEST_SOURCES})
-
-    # ----- RUN TESTS ----- #
-    add_custom_command(TARGET DetectionFormatsTests
-        POST_BUILD
-        COMMAND DetectionFormatsTests
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Running DetectionFormatsTests" VERBATIM
-    )
-
-    # ----- RUN COVERAGE ----- #
-    if(SUPPORT_COVERAGE)
-
-        option(RUN_COVERAGE "Run Coverage Report (requires lcov installed)" OFF)
-
-        if(RUN_COVERAGE)
-            add_custom_target(coverage-report ALL
-              DEPENDS DetectionFormatsTests
-              COMMAND /bin/sh
-              ${PROJECT_SOURCE_DIR}/generate_coverage.sh
-              COMMENT "Capture/Report Coverage Info" VERBATIM
-            )
-
-        endif (RUN_COVERAGE)
-
-    endif (SUPPORT_COVERAGE)
-endif()
-
-# ----- CPPCHECK ----- #
-option(RUN_CPPCHECK "Run CPP Checks (requires cppcheck installed)" OFF)
-
-if(RUN_CPPCHECK)
-
-    file(GLOB CPPCHECK_SRCS "${PROJECT_SOURCE_DIR}/include/*.h" "${PROJECT_SOURCE_DIR}/src/*.cpp")
-
-    add_custom_target(cppcheck ALL
-      DEPENDS DetectionFormats
-      COMMAND cppcheck
-      --enable=warning,performance,portability
-      --language=c++
-      --std=c++11
-      --template="[{severity}][{id}] {message} {callstack} \(On {file}:{line}\)"
-      --verbose
-      --suppress=nullPointerRedundantCheck
-      --error-exitcode=1
-      ${CPPCHECK_SRCS}
-      COMMENT "Running cppcheck" VERBATIM
-    )
-endif()
-
-# ----- CPPLINT ----- #
-option(RUN_CPPLINT "Run CPP Checks (requires cpplint and python installed)" OFF)
-
-if(RUN_CPPLINT)
-
-    set(CPPLINT_PATH "${CURRENT_SOURCE_DIR}/lib/cpplint/cpplint.py" CACHE FILEPATH "Path to cpplint")
-    file(GLOB CPPLINT_SRCS "${PROJECT_SOURCE_DIR}/include/*.h"
-                           "${PROJECT_SOURCE_DIR}/src/*.cpp")
-
-    add_custom_target(cpplint ALL
-      DEPENDS DetectionFormats
-      COMMAND /usr/bin/python "${CPPLINT_PATH}"
-      --filter=-whitespace/tab,-legal/copyright,-build/c++11,-build/header_guard,-readability/fn_size,-runtime/references
-      ${CPPLINT_SRCS}
-      COMMENT "Running cpplint" VERBATIM
-    )
-endif()
-
-# ----- DOCUMENTATION ----- #
-option(GENERATE_DOCUMENTATION "Create and install the HTML based API documentation (requires Doxygen)" OFF)
-
-if(GENERATE_DOCUMENTATION)
-
-    # ----- LOOK FOR DOXYGEN ----- #
-    find_package(Doxygen REQUIRED)
-
-    set(doxyfile_in ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
-    set(doxyfile ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
-
-    configure_file(${doxyfile_in} ${doxyfile} @ONLY)
-
-    add_custom_target(doc ALL
-        COMMAND ${DOXYGEN_EXECUTABLE} ${doxyfile}
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Generating API documentation with Doxygen"
-        VERBATIM)
-
-    install(
-        DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
-        DESTINATION doc/${PROJECT_NAME}
-    )
-endif()
-
-# ----- INSTALL RULES ----- #
-# Layout. This works for all platforms:
-#   * <prefix>/lib/<PROJECT-NAME>
-#   * <prefix>/lib/
-#   * <prefix>/include/
-set(config_install_dir "lib/${PROJECT_NAME}")
-set(include_install_dir "include")
-
-set(generated_dir "${CMAKE_CURRENT_BINARY_DIR}/generated")
-
-# ----- Configuration ----- #
-set(version_config "${generated_dir}/${PROJECT_NAME}ConfigVersion.cmake")
-set(project_config "${generated_dir}/${PROJECT_NAME}Config.cmake")
-set(targets_export_name "${PROJECT_NAME}Targets")
-set(namespace "${PROJECT_NAME}::")
-
-# Include module with function 'write_basic_package_version_file'
-include(CMakePackageConfigHelpers)
-
-# Configure '<PROJECT-NAME>ConfigVersion.cmake'
-# Note: PROJECT_VERSION is used as a VERSION
-write_basic_package_version_file(
-    "${version_config}" COMPATIBILITY SameMajorVersion
-)
-
-# Configure '<PROJECT-NAME>Config.cmake'
-# Use variables:
-#   * targets_export_name
-#   * PROJECT_NAME
-configure_package_config_file(
-    "Config.cmake.in"
-    "${project_config}"
-    INSTALL_DESTINATION "${config_install_dir}"
-)
-
-# Targets:
-#   * <prefix>/lib/libDetectionFormats.a
-#   * header location after install: <prefix>/include/*.h
-install(
-    TARGETS DetectionFormats
-    EXPORT "${targets_export_name}"
-    LIBRARY DESTINATION "lib"
-    ARCHIVE DESTINATION "lib"
-    RUNTIME DESTINATION "bin"
-    INCLUDES DESTINATION "${include_install_dir}"
-)
+# ----- BUILD LIBRARY ----- #
+include(${CMAKE_DIR}/build_lib.cmake)
 
-# Headers:
-#   * *.h-> <prefix>/include/*.h
-install(
-    FILES ${HDRS}
-    DESTINATION "${include_install_dir}/${PROJECT_NAME}"
-)
+# ----- RUN CPPCHECK ----- #
+include(${CMAKE_DIR}/cppcheck.cmake)
 
-install(
-    DIRECTORY ${RAPIDJSON_PATH}
-    DESTINATION "${include_install_dir}"
-    )
+# ----- RUN CPPLINT ----- #
+include(${CMAKE_DIR}/cpplint.cmake)
 
-# Export headers:
-#   * ${CMAKE_CURRENT_BINARY_DIR}/DetectionFormats_export.h -> <prefix>/include/DetectionFormats_export.h
-install(
-    FILES
-        "${CMAKE_CURRENT_BINARY_DIR}/DetectionFormats_export.h"
-    DESTINATION "${include_install_dir}"
-)
+# ----- RUN UNIT TESTS ----- #
+file(GLOB TESTS ${PROJECT_SOURCE_DIR}/tests/*.cpp)
+# WARNING: linking order of libraries matters for G++
+set(TEST_LIBRARIES ${SuperEasyJSON_LIBRARIES} ${util_LIBRARIES} ${DetectionFormats_LIBRARIES})
+include(${CMAKE_DIR}/test.cmake)
 
-# Config
-#   * <prefix>/lib/DetectionFormats/DetectionFormatsConfig.cmake
-#   * <prefix>/lib/DetectionFormats/DetectionFormatsConfigVersion.cmake
-install(
-    FILES "${project_config}" "${version_config}"
-    DESTINATION "${config_install_dir}"
-)
+# ----- GENERATE DOCUMENTATION ----- #
+set(DOC_DIRS "${PROJECT_SOURCE_DIR}/include/")
+include(${CMAKE_DIR}/documentation.cmake)
 
-# Config
-#   * <prefix>/lib/DetectionFormats/DetectionFormatsTargets.cmake
-install(
-    EXPORT "${targets_export_name}"
-    NAMESPACE "${namespace}"
-    DESTINATION "${config_install_dir}"
-)
+# ----- INSTALL LIBRARY ----- #
+include(${CMAKE_DIR}/install_lib.cmake)