Improve cmake and directory organization.

CMakeLists.txt

@@ -4,11 +4,8 @@ cmake_minimum_required(VERSION 2.8.7)
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 include(ClangTools)
 
-# Enable Clang auto-formatting, defaults to on. 
 option(ENABLE_AUTOFORMAT "Enable automatic formatting and replacement with clang-format." ON)
-# Enable Clang auto-linting, defaults to off.
 option(ENABLE_AUTOLINT "Enable automatic linting and warning with clang-tidy. " OFF)
-# Enable static stack analyzer, defaults to off.
 option(ENABLE_STACK_ANALYSIS "Enable stack analysis. Requires gcc." OFF)
 
 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
@@ -17,68 +14,22 @@ endif()
 
 add_subdirectory(third_party/googletest)
 
-include_directories(SYSTEM ${gtest_SOURCE_DIR} ${gtest_SOURCE_DIR}/include)
-include_directories(SYSTEM "${PROJECT_SOURCE_DIR}/third_party/eigen/")
-include_directories(SYSTEM "${PROJECT_SOURCE_DIR}/third_party/cereal/include")
-include_directories(SYSTEM "${PROJECT_SOURCE_DIR}/third_party/fast-cpp-csv-parser/")
+add_library(albatross INTERFACE)
+target_include_directories(albatross INTERFACE
+  "${PROJECT_SOURCE_DIR}/include"
+  )
+target_include_directories(albatross SYSTEM INTERFACE
+  "${PROJECT_SOURCE_DIR}/third_party/eigen/"
+  "${PROJECT_SOURCE_DIR}/third_party/cereal/include"
+  "${PROJECT_SOURCE_DIR}/third_party/fast-cpp-csv-parser/"
+  )
+
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror -fexceptions -frtti")
 set(CMAKE_CXX_FLAGS "-std=c++14 -Wshadow -Wswitch-default -Wswitch-enum -Wundef -Wpointer-arith -Wcast-align -Wformat=2 -Wredundant-decls ${CMAKE_CXX_FLAGS}")
 set("LOG_LEVEL=8")
 
-include_directories("${PROJECT_SOURCE_DIR}/albatross")
 include(${PROJECT_SOURCE_DIR}/cmake/FindGFlags.cmake)
 
-set(albatross_HEADERS
-    albatross/cereal/eigen.h
-    albatross/cereal/traits.h
-    albatross/core/dataset.h
-    albatross/core/declarations.h
-    albatross/core/distribution.h
-    albatross/core/fit_model.h
-    albatross/core/indexing.h
-    albatross/core/keys.h
-    albatross/core/model.h
-    albatross/core/parameter_handling_mixin.h
-    albatross/core/parameter_macros.h
-    albatross/core/prediction.h
-    albatross/core/priors.h
-    albatross/core/serialize.h
-    albatross/core/traits.h
-    albatross/covariance_functions/call_trace.h
-    albatross/covariance_functions/covariance_function.h
-    albatross/covariance_functions/distance_metrics.h
-    albatross/covariance_functions/noise.h
-    albatross/covariance_functions/polynomials.h
-    albatross/covariance_functions/radial.h
-    albatross/covariance_functions/scaling_function.h
-    albatross/covariance_functions/traits.h
-    albatross/csv_utils.h
-    albatross/eigen/serializable_diagonal_matrix.h
-    albatross/eigen/serializable_ldlt.h
-    albatross/eigen_utils.h
-    albatross/evaluation/cross_validation.h
-    albatross/evaluation/cross_validation_utils.h
-    albatross/evaluation/evaluate.h
-    albatross/evaluation/folds.h
-    albatross/map_utils.h
-    albatross/models/gp.h
-    albatross/models/least_squares.h
-    albatross/models/ransac.h
-    albatross/random_utils.h
-    albatross/tune.h
-    albatross/tuning_metrics.h
-    examples/example_utils.h
-    examples/sinc_example_utils.h
-    examples/temperature_example/temperature_example_utils.h
-    tests/mock_model.h
-    tests/test_core_distribution.h
-    tests/test_models.h
-    tests/test_serialize.h
-    tests/test_utils.h
-)
-
-add_custom_target(albatross DEPENDS ${albatross_HEADERS} COMMENT "albatross dependencies")
-
 add_subdirectory(tests)
 add_subdirectory(examples)

cmake/ClangTools.cmake

@@ -11,7 +11,7 @@
 
 # Do not use clang tooling when cross compiling.
 if(CMAKE_CROSSCOMPILING)
-    return()
+  return()
 endif(CMAKE_CROSSCOMPILING)
 
 ################################################################################
@@ -21,27 +21,23 @@ endif(CMAKE_CROSSCOMPILING)
 # Check for Clang format
 set(CLANG_FORMAT_PATH "NOTSET" CACHE STRING "Absolute path to the clang-format executable")
 if("${CLANG_FORMAT_PATH}" STREQUAL "NOTSET")
-    find_program(CLANG_FORMAT NAMES
-        clang-format39 clang-format-3.9
-        clang-format38 clang-format-3.8
-        clang-format37 clang-format-3.7
-        clang-format36 clang-format-3.6
-        clang-format35 clang-format-3.5
-        clang-format34 clang-format-3.4
-        clang-format)
-    message(STATUS "Using clang format: ${CLANG_FORMAT}")
-    if("${CLANG_FORMAT}" STREQUAL "CLANG_FORMAT-NOTFOUND")
-        message(WARNING "Could not find 'clang-format' please set CLANG_FORMAT_PATH:STRING")
-    else()
-        set(CLANG_FORMAT_PATH ${CLANG_FORMAT})
-        message(STATUS "Found: ${CLANG_FORMAT_PATH}")
-    endif()
+  find_program(CLANG_FORMAT NAMES
+    clang-format-6.0
+    clang-format-4.0
+    )
+  message(STATUS "Using clang format: ${CLANG_FORMAT}")
+  if("${CLANG_FORMAT}" STREQUAL "CLANG_FORMAT-NOTFOUND")
+    message(WARNING "Could not find 'clang-format' please set CLANG_FORMAT_PATH:STRING")
+  else()
+    set(CLANG_FORMAT_PATH ${CLANG_FORMAT})
+    message(STATUS "Found: ${CLANG_FORMAT_PATH}")
+  endif()
 else()
-    if(NOT EXISTS ${CLANG_FORMAT_PATH})
-        message(WARNING "Could not find 'clang-format': ${CLANG_FORMAT_PATH}")
-    else()
-        message(STATUS "Found: ${CLANG_FORMAT_PATH}")
-    endif()
+  if(NOT EXISTS ${CLANG_FORMAT_PATH})
+    message(WARNING "Could not find 'clang-format': ${CLANG_FORMAT_PATH}")
+  else()
+    message(STATUS "Found: ${CLANG_FORMAT_PATH}")
+  endif()
 endif()
 
 ################################################################################
@@ -50,24 +46,24 @@ endif()
 
 
 if (EXISTS ${CLANG_FORMAT_PATH})
-    # Format all files .cc files (and their headers) in project
-    add_custom_target(clang-format-all
-        COMMAND git ls-files -- '../*.cc' '../*.h'
-        | sed 's/^...//' | sed 's\#\^\#${CMAKE_SOURCE_DIR}/\#'
-        | xargs "${CLANG_FORMAT_PATH}" -i
-        )
-    # In-place format *.cc files that differ from master, and are not listed as
-    # being DELETED.
-    add_custom_target(clang-format-diff
-        COMMAND git diff --diff-filter=ACMRTUXB --name-only master -- '../*.cc' '../*.h'
-        | sed 's\#\^\#${CMAKE_SOURCE_DIR}/\#'
-        | xargs "${CLANG_FORMAT_PATH}" -i
-        )
+  # Format all files .cc files (and their headers) in project
+  add_custom_target(clang-format-all
+    COMMAND git ls-files -- '../*.cc' '../*.h'
+    | sed 's/^...//' | sed 's\#^\#${CMAKE_SOURCE_DIR}/\#'
+    | xargs "${CLANG_FORMAT_PATH}" -i
+    )
+  # In-place format *.cc files that differ from master, and are not listed as
+  # being DELETED.
+  add_custom_target(clang-format-diff
+    COMMAND git diff --diff-filter=ACMRTUXB --name-only master -- '../*.cc' '../*.h'
+    | sed 's\#^\#${CMAKE_SOURCE_DIR}/\#'
+    | xargs "${CLANG_FORMAT_PATH}" -i
+    )
 endif()
 if (EXISTS ${CPPCHECK_PATH})
-    add_custom_target(cppcheck-all
-        COMMAND git ls-files -- '../*.cc' '../*.h'
-        | ${CPPCHECK_PATH} --enable=all --std=c++14 -I../include -isystem../third_party/eigen -q --file-list=-
-        )
+  add_custom_target(cppcheck-all
+    COMMAND git ls-files -- '../*.cc' '../*.h'
+    | ${CPPCHECK_PATH} --enable=all --std=c++14 -I../include -isystem../third_party/eigen -q --file-list=-
+    )
 endif()
 

examples/CMakeLists.txt

@@ -1,96 +1,60 @@
-include_directories(SYSTEM "${PROJECT_SOURCE_DIR}/third_party/fast-cpp-csv-parser/")
-
-set(example_HEADERS
-    example_utils.h
-    sinc_example_utils.h
-    CACHE INTERNAL ""
-)
-
 add_executable(sinc_example
-    EXCLUDE_FROM_ALL
-    sinc_example.cc
-)
-
-add_dependencies(sinc_example
-    albatross
-)
-
-target_link_libraries(sinc_example m gflags pthread nlopt)
+  sinc_example.cc
+  )
+target_link_libraries(sinc_example
+  albatross
+  gflags
+  pthread
+  nlopt
+  )
+add_custom_target(run_sinc_example
+  DEPENDS sinc_example
+  COMMAND sinc_example -input ${PROJECT_SOURCE_DIR}/examples/sinc_input.csv -output ./sinc_predictions.csv -tune
+  COMMENT "Running sinc_example"
+  )
 
-add_custom_target(
-    run_sinc_example ALL
-    DEPENDS ${example_HEADERS}
-    COMMAND sinc_example -input ${PROJECT_SOURCE_DIR}/examples/sinc_input.csv -output ./sinc_predictions.csv -tune
-    COMMENT "Running sinc_example"
-)
-
-add_dependencies(run_sinc_example
-    sinc_example
-)
 
 add_executable(inspection_example
-    EXCLUDE_FROM_ALL
-    inspection.cc
-)
-
-add_dependencies(inspection_example
-    albatross
-)
-
-target_link_libraries(inspection_example m gflags pthread)
-
-add_custom_target(
-    run_inspection_example ALL
-    DEPENDS ${example_HEADERS}
-    COMMAND inspection_example -input ${PROJECT_SOURCE_DIR}/examples/inspection_input.csv
-    COMMENT "Running inspection_example"
-)
-
-add_dependencies(run_inspection_example
-    inspection_example
-)
+  inspection.cc
+  )
+target_link_libraries(inspection_example
+  albatross
+  gflags
+  pthread
+  )
+add_custom_target(run_inspection_example
+  DEPENDS inspection_example
+  COMMAND inspection_example -input ${PROJECT_SOURCE_DIR}/examples/inspection_input.csv
+  COMMENT "Running inspection_example"
+  )
 
 
 add_executable(temperature_example
-    EXCLUDE_FROM_ALL
-    temperature_example/temperature_example.cc
-)
-
-add_dependencies(temperature_example
-    albatross
-)
-
-target_link_libraries(temperature_example m gflags pthread nlopt)
-
-add_custom_target(
-    run_temperature_example ALL
-    DEPENDS ${example_HEADERS}
-    COMMAND temperature_example -input ${PROJECT_SOURCE_DIR}/examples/temperature_example/gsod.csv -predict ${PROJECT_SOURCE_DIR}/examples/temperature_example/prediction_locations.csv -output ./test_temperature_predictions.csv -thin 5
-    COMMENT "Running temperature_example"
-)
+  temperature_example/temperature_example.cc
+  )
+target_link_libraries(temperature_example
+  albatross
+  gflags
+  pthread
+  nlopt
+  )
+add_custom_target(run_temperature_example
+  DEPENDS temperature_example
+  COMMAND temperature_example -input ${PROJECT_SOURCE_DIR}/examples/temperature_example/gsod.csv -predict ${PROJECT_SOURCE_DIR}/examples/temperature_example/prediction_locations.csv -output ./test_temperature_predictions.csv -thin 5
+  COMMENT "Running temperature_example"
+  )
 
-add_dependencies(run_temperature_example
-    temperature_example
-)
 
 add_executable(call_trace_example
-    EXCLUDE_FROM_ALL
-    call_trace_example.cc
-)
-
-add_dependencies(call_trace_example
-    albatross
-)
-
-target_link_libraries(call_trace_example m gflags pthread)
-
-add_custom_target(
-    run_call_trace_example ALL
-    DEPENDS ${example_HEADERS}
-    COMMAND call_trace_example
-    COMMENT "Running call_trace_example"
-)
-
-add_dependencies(run_call_trace_example
-    call_trace_example
-)
+  call_trace_example.cc
+  )
+target_link_libraries(call_trace_example
+  albatross
+  gflags
+  pthread
+  )
+add_custom_target(run_call_trace_example
+  DEPENDS call_trace_example
+  COMMAND call_trace_example
+  COMMENT "Running call_trace_example"
+  )

examples/call_trace_example.cc

@@ -10,16 +10,15 @@
  * WARRANTIES OF MERCHANTABILITY AND/OR FITNESS FOR A PARTICULAR PURPOSE.
  */
 
-#include "CovarianceFunctions"
+#include <albatross/CovarianceFunctions>
 
 namespace albatross {
 
 class LinearScalar : public ScalingFunction {
 public:
   std::string get_name() const override { return "linear_scalar"; }
 
-  double _call_impl((const double &x) const {
-    return 1. + 3. * x; }
+  double _call_impl(const double &x) const { return 1. + 3. * x; }
 };
 
 auto complicated_covariance_function() {
@@ -30,7 +29,7 @@ auto complicated_covariance_function() {
 
   return (constant + squared_exp) * linear_scalar;
 }
-}
+} // namespace albatross
 
 int main() {