rename src/code_base -> src/bmdscore (#73)

* reformat * move over some of the functions * see if a few more files can be deleted * remove? * move test scripts * move pybind11.cmake? * rename src/code_base -> src/bmdscore * added project name to CMake file --------- Co-authored-by: Cody Simmons <[email protected]>
USEPA · Oct 29, 2024 · d77f3be · d77f3be
1 parent 582a33d
commit d77f3be
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Showing 51 changed files with 17 additions and 15 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -63,11 +63,11 @@ find_library(NLOPT_LIB NAMES NLopt nlopt libnlopt  REQUIRED HINTS ${NLOPT_DIR})
 
 project(bmdscore)
 
-include_directories("${CMAKE_SOURCE_DIR}/src/code_base" "${CMAKE_SOURCE_DIR}/src/include" ${EIGEN_DIR} ${NLOPT_DIR}/../include ${NLOPT_DIR} ${GSL_DIR})
+include_directories("${CMAKE_SOURCE_DIR}/src/bmdscore" "${CMAKE_SOURCE_DIR}/src/include" ${EIGEN_DIR} ${NLOPT_DIR}/../include ${NLOPT_DIR} ${GSL_DIR})
 link_directories(${GSL_LIB_DIR} ${NLOPT_LIB_DIR})
 
-file (GLOB SOURCE_FILES "${CMAKE_SOURCE_DIR}/src/code_base/*.cpp")
-file (GLOB HEADER_FILES "src/include/*.h" "src/code_base/*.h" ${EIGEN_DIR})
+file (GLOB SOURCE_FILES "${CMAKE_SOURCE_DIR}/src/bmdscore/*.cpp")
+file (GLOB HEADER_FILES "src/include/*.h" "src/bmdscore/*.h" ${EIGEN_DIR})
 file (GLOB PYTHON_FILES "src/pybmdscpp/*.cpp" "src/pybmdscpp/*.h")
 
 # Set up such that XCode organizes the files

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -31,6 +31,8 @@ IF(WIN32)
   add_compile_definitions(RBMDS_EXPORTS)
 ENDIF()
 
+project(bmdscore)
+
 # Find libraries
 IF(WIN32)
   find_library(GSL_LIB gsl REQUIRED HINTS ${GSL_DIR})
@@ -43,10 +45,10 @@ find_library(NLOPT_LIB NAMES NLopt nlopt libnlopt  REQUIRED HINTS ${NLOPT_DIR})
 link_directories(${GSL_LIB_DIR} ${NLOPT_LIB_DIR})
 
 # Include dir
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/code_base ${CMAKE_CURRENT_SOURCE_DIR}/include ${EIGEN_DIR} ${GSL_DIR} ${NLOPT_DIR} ${NLOPT_DIR}/../include)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/bmdscore ${CMAKE_CURRENT_SOURCE_DIR}/include ${EIGEN_DIR} ${GSL_DIR} ${NLOPT_DIR} ${NLOPT_DIR}/../include)
 
 # Headers
-set(PROJECT_SOURCE_DIR "code_base")
+set(PROJECT_SOURCE_DIR "bmdscore")
 set(PROJECT_INCLUDE_DIR "include")
 
 # Source files
@@ -163,7 +165,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
 add_custom_target(coverage
 	COMMAND ${CMAKE_COMMAND} -E env "LCOV_EXCL_BR_LINE=:${PROJECT_SOURCE_DIR}/../unitTests/*" gcov -b ${PROJECT_SOURCE_DIR}../unitTests ${PROJECT_SOURCE_DIR}/../build/CMakeFiles/unit_tests.dir/unitTests/test_main.cpp.gcno ${PROJECT_SOURCE_DIR}/../build/CMakeFiles/bmdscore.dir/*.gcno
 
-	COMMAND lcov -d ./CMakeFiles/bmdscore.dir/code_base/ -c -o ./coverage.info
+	COMMAND lcov -d ./CMakeFiles/bmdscore.dir/bmdscore/ -c -o ./coverage.info
 	COMMAND lcov -r ./coverage.info ${TEST_EXC} ${EIGEN_DIR} '*gcc*' -o ./coverage.info --ignore-errors unused
 	COMMAND lcov -r ./coverage.info
 	COMMAND lcov -r ./coverage.info -o ./coverage.info
@@ -186,7 +188,7 @@ add_custom_target(run_tests
 add_custom_target(run_tests_with_coverage
 	COMMAND ./unit_tests
 	COMMAND ${CMAKE_COMMAND} -E env "LCOV_EXCL_BR_LINE=:${PROJECT_SOURCE_DIR}/../unitTests/*" gcov -b ${PROJECT_SOURCE_DIR}../unitTests ${PROJECT_SOURCE_DIR}/../build/CMakeFiles/unit_tests.dir/unitTests/test_main.cpp.gcno ${PROJECT_SOURCE_DIR}/../build/CMakeFiles/bmdscore.dir/*.gcno
-	COMMAND lcov -d ./CMakeFiles/bmdscore.dir/code_base/ -c -o ./coverage.info
+	COMMAND lcov -d ./CMakeFiles/bmdscore.dir/bmdscore/ -c -o ./coverage.info
 	COMMAND lcov -r ./coverage.info ${TEST_EXC} ${EIGEN_DIR} '*gcc*' -o ./coverage.info --ignore-errors unused
 	COMMAND genhtml ./coverage.info -o ./coverage
 	WORKING_DIRECTORY ./  #${PROJECT_BINARY_DIR}

diff --git a/src/Makevars b/src/Makevars
@@ -1,15 +1,15 @@
 DISTRO = $(shell uname)
 
 ifeq ($(DISTRO), Linux)
-	PKG_CPPFLAGS =  -I"./include" -I"./code_base"   -ftree-vectorize -Os -march=native
+	PKG_CPPFLAGS =  -I"./include" -I"./bmdscore"   -ftree-vectorize -Os -march=native
 	PKG_CPPFLAGS +=  $(shell pkg-config --cflags nlopt gsl) -DR_COMPILATION -Wno-ignored-attributes  -flto -fopenmp
 	PKG_LIBS     =   $(shell pkg-config --libs nlopt gsl)
 else
-	PKG_CPPFLAGS =  -I"./code_base" -I"./include"   -ftree-vectorize -Os -fopenmp
+	PKG_CPPFLAGS =  -I"./bmdscore" -I"./include"   -ftree-vectorize -Os -fopenmp
 	PKG_CPPFLAGS +=  -DR_COMPILATION -Wno-ignored-attributes  -DNDEBUG $(shell pkg-config --cflags nlopt gsl) #-fopenmp
 	PKG_LIBS     = -lomp  $(shell pkg-config --libs nlopt gsl)
 endif
 
 MAIN         = $(wildcard *.cpp)
-MAIN_CODE    = $(wildcard code_base/*.cpp)
+MAIN_CODE    = $(wildcard bmdscore/*.cpp)
 OBJECTS      = $(MAIN:.cpp=.o) $(MAIN_CODE:.cpp=.o)
diff --git a/src/Makevars.in b/src/Makevars.in
@@ -1,4 +1,4 @@
-PKG_CXXFLAGS =  -I./code_base -I./include @OPENMP@ @NLOPT_CPPFLAGS@ @GSL_CPPFLAGS@ -DR_COMPILATION
+PKG_CXXFLAGS =  -I./bmdscore -I./include @OPENMP@ @NLOPT_CPPFLAGS@ @GSL_CPPFLAGS@ -DR_COMPILATION
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @NLOPT_LIBS@  @GSL_LIBS@ @OPENMP@
 
 # Include all C++ files in src/ and its subdirectories

diff --git a/src/code_base/DichGammaBMD_NC.cpp → src/bmdscore/DichGammaBMD_NC.cpp b/src/code_base/DichGammaBMD_NC.cpp → src/bmdscore/DichGammaBMD_NC.cpp
diff --git a/src/code_base/DichLogProbitBMD_NC.cpp → src/bmdscore/DichLogProbitBMD_NC.cpp b/src/code_base/DichLogProbitBMD_NC.cpp → src/bmdscore/DichLogProbitBMD_NC.cpp
diff --git a/src/code_base/DichLogisticBMD_NC.cpp → src/bmdscore/DichLogisticBMD_NC.cpp b/src/code_base/DichLogisticBMD_NC.cpp → src/bmdscore/DichLogisticBMD_NC.cpp
diff --git a/src/code_base/DichProbitBMD_NC.cpp → src/bmdscore/DichProbitBMD_NC.cpp b/src/code_base/DichProbitBMD_NC.cpp → src/bmdscore/DichProbitBMD_NC.cpp
diff --git a/src/code_base/DichQlinearBMD_NC.cpp → src/bmdscore/DichQlinearBMD_NC.cpp b/src/code_base/DichQlinearBMD_NC.cpp → src/bmdscore/DichQlinearBMD_NC.cpp
diff --git a/src/code_base/DichWeibullBMD_NC.cpp → src/bmdscore/DichWeibullBMD_NC.cpp b/src/code_base/DichWeibullBMD_NC.cpp → src/bmdscore/DichWeibullBMD_NC.cpp
diff --git a/src/code_base/IDPrior.cpp → src/bmdscore/IDPrior.cpp b/src/code_base/IDPrior.cpp → src/bmdscore/IDPrior.cpp
diff --git a/src/code_base/IDPriorMCMC.cpp → src/bmdscore/IDPriorMCMC.cpp b/src/code_base/IDPriorMCMC.cpp → src/bmdscore/IDPriorMCMC.cpp
diff --git a/src/code_base/Makefile.am → src/bmdscore/Makefile.am b/src/code_base/Makefile.am → src/bmdscore/Makefile.am
@@ -1,6 +1,6 @@
-noinst_LTLIBRARIES = libBMDS.la 
+noinst_LTLIBRARIES = libBMDS.la
 
-AM_CPPFLAGS= -I$(top_srcdir)/code_base -I$(top_srcdir)/include  -I$(EIGEN_INCLUDE)
+AM_CPPFLAGS= -I$(top_srcdir)/bmdscore -I$(top_srcdir)/include  -I$(EIGEN_INCLUDE)
 AM_CPPFLAGS+=  -O3 -funroll-loops -std=c++11
 AM_CPPFLAGS+= @OPENMP_CFLAGS@ -Wno-ignored-attributes -DEIGEN_NO_DEBUG -march=native
 

diff --git a/src/code_base/analysis_of_deviance.cpp → src/bmdscore/analysis_of_deviance.cpp b/src/code_base/analysis_of_deviance.cpp → src/bmdscore/analysis_of_deviance.cpp
diff --git a/src/code_base/analysis_of_deviance.h → src/bmdscore/analysis_of_deviance.h b/src/code_base/analysis_of_deviance.h → src/bmdscore/analysis_of_deviance.h
diff --git a/src/code_base/bmdStruct.cpp → src/bmdscore/bmdStruct.cpp b/src/code_base/bmdStruct.cpp → src/bmdscore/bmdStruct.cpp
diff --git a/src/code_base/bmdStruct.h → src/bmdscore/bmdStruct.h b/src/code_base/bmdStruct.h → src/bmdscore/bmdStruct.h
diff --git a/src/code_base/bmds_helper.cpp → src/bmdscore/bmds_helper.cpp b/src/code_base/bmds_helper.cpp → src/bmdscore/bmds_helper.cpp
diff --git a/src/code_base/bmds_helper.h → src/bmdscore/bmds_helper.h b/src/code_base/bmds_helper.h → src/bmdscore/bmds_helper.h
diff --git a/src/code_base/continuous_clean_aux.cpp → src/bmdscore/continuous_clean_aux.cpp b/src/code_base/continuous_clean_aux.cpp → src/bmdscore/continuous_clean_aux.cpp
diff --git a/src/code_base/continuous_clean_aux.h → src/bmdscore/continuous_clean_aux.h b/src/code_base/continuous_clean_aux.h → src/bmdscore/continuous_clean_aux.h
diff --git a/src/code_base/continuous_entry_code.cpp → src/bmdscore/continuous_entry_code.cpp b/src/code_base/continuous_entry_code.cpp → src/bmdscore/continuous_entry_code.cpp
diff --git a/src/code_base/continuous_entry_code.h → src/bmdscore/continuous_entry_code.h b/src/code_base/continuous_entry_code.h → src/bmdscore/continuous_entry_code.h
diff --git a/src/code_base/continuous_model_functions.cpp → src/bmdscore/continuous_model_functions.cpp b/src/code_base/continuous_model_functions.cpp → src/bmdscore/continuous_model_functions.cpp
diff --git a/src/code_base/continuous_model_functions.h → src/bmdscore/continuous_model_functions.h b/src/code_base/continuous_model_functions.h → src/bmdscore/continuous_model_functions.h
diff --git a/src/code_base/dichotomous_entry_code.cpp → src/bmdscore/dichotomous_entry_code.cpp b/src/code_base/dichotomous_entry_code.cpp → src/bmdscore/dichotomous_entry_code.cpp
diff --git a/src/code_base/dichotomous_entry_code.h → src/bmdscore/dichotomous_entry_code.h b/src/code_base/dichotomous_entry_code.h → src/bmdscore/dichotomous_entry_code.h
diff --git a/src/code_base/framework.h → src/bmdscore/framework.h b/src/code_base/framework.h → src/bmdscore/framework.h
diff --git a/src/code_base/gradient.cpp → src/bmdscore/gradient.cpp b/src/code_base/gradient.cpp → src/bmdscore/gradient.cpp
diff --git a/src/code_base/gradient.h → src/bmdscore/gradient.h b/src/code_base/gradient.h → src/bmdscore/gradient.h
diff --git a/src/code_base/helperfunctions.cpp → src/bmdscore/helperfunctions.cpp b/src/code_base/helperfunctions.cpp → src/bmdscore/helperfunctions.cpp
diff --git a/src/code_base/list_r_conversion.h → src/bmdscore/list_r_conversion.h b/src/code_base/list_r_conversion.h → src/bmdscore/list_r_conversion.h
diff --git a/src/code_base/lognormalModels.cpp → src/bmdscore/lognormalModels.cpp b/src/code_base/lognormalModels.cpp → src/bmdscore/lognormalModels.cpp
diff --git a/src/code_base/lognormal_EXP_NC.cpp → src/bmdscore/lognormal_EXP_NC.cpp b/src/code_base/lognormal_EXP_NC.cpp → src/bmdscore/lognormal_EXP_NC.cpp
diff --git a/src/code_base/lognormal_HILL_NC.cpp → src/bmdscore/lognormal_HILL_NC.cpp b/src/code_base/lognormal_HILL_NC.cpp → src/bmdscore/lognormal_HILL_NC.cpp
diff --git a/src/code_base/lognormal_POLYNOMIAL_NC.cpp → src/bmdscore/lognormal_POLYNOMIAL_NC.cpp b/src/code_base/lognormal_POLYNOMIAL_NC.cpp → src/bmdscore/lognormal_POLYNOMIAL_NC.cpp
diff --git a/src/code_base/lognormal_POWER_NC.cpp → src/bmdscore/lognormal_POWER_NC.cpp b/src/code_base/lognormal_POWER_NC.cpp → src/bmdscore/lognormal_POWER_NC.cpp
diff --git a/src/code_base/normalModels.cpp → src/bmdscore/normalModels.cpp b/src/code_base/normalModels.cpp → src/bmdscore/normalModels.cpp
diff --git a/src/code_base/normal_EXP_NC.cpp → src/bmdscore/normal_EXP_NC.cpp b/src/code_base/normal_EXP_NC.cpp → src/bmdscore/normal_EXP_NC.cpp
diff --git a/src/code_base/normal_FUNL_NC.cpp → src/bmdscore/normal_FUNL_NC.cpp b/src/code_base/normal_FUNL_NC.cpp → src/bmdscore/normal_FUNL_NC.cpp
diff --git a/src/code_base/normal_HILL_NC.cpp → src/bmdscore/normal_HILL_NC.cpp b/src/code_base/normal_HILL_NC.cpp → src/bmdscore/normal_HILL_NC.cpp
diff --git a/src/code_base/normal_POLYNOMIAL_NC.cpp → src/bmdscore/normal_POLYNOMIAL_NC.cpp b/src/code_base/normal_POLYNOMIAL_NC.cpp → src/bmdscore/normal_POLYNOMIAL_NC.cpp
diff --git a/src/code_base/normal_POWER_NC.cpp → src/bmdscore/normal_POWER_NC.cpp b/src/code_base/normal_POWER_NC.cpp → src/bmdscore/normal_POWER_NC.cpp
diff --git a/src/code_base/normal_likelihoods.cpp → src/bmdscore/normal_likelihoods.cpp b/src/code_base/normal_likelihoods.cpp → src/bmdscore/normal_likelihoods.cpp
diff --git a/src/code_base/pch.cpp → src/bmdscore/pch.cpp b/src/code_base/pch.cpp → src/bmdscore/pch.cpp
diff --git a/src/code_base/pch.h → src/bmdscore/pch.h b/src/code_base/pch.h → src/bmdscore/pch.h
diff --git a/src/code_base/stdafx.cpp → src/bmdscore/stdafx.cpp b/src/code_base/stdafx.cpp → src/bmdscore/stdafx.cpp
diff --git a/src/code_base/stdafx.h → src/bmdscore/stdafx.h b/src/code_base/stdafx.h → src/bmdscore/stdafx.h
diff --git a/src/code_base/targetver.h → src/bmdscore/targetver.h b/src/code_base/targetver.h → src/bmdscore/targetver.h
diff --git a/src/code_base/.DS_Store b/src/code_base/.DS_Store
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
@@ -6,7 +6,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 
 project(test_cpp)
 
-set(CPP_BASE ../) 
+set(CPP_BASE ../)
 
 IF(DEFINED ENV{EIGEN_DIR})
   set(EIGEN_DIR $ENV{EIGEN_DIR})
@@ -34,7 +34,7 @@ ELSE()
 ENDIF()
 find_library(NLOPT_LIB NAMES NLopt nlopt libnlopt  REQUIRED HINTS ${NLOPT_DIR})
 
-include_directories(${CPP_BASE}/tests/src ${CPP_BASE}/build ${CPP_BASE}/include ${CPP_BASE}/code_base ${EIGEN_DIR} ${NLOPT_DIR}/../include ${GSL_DIR})
+include_directories(${CPP_BASE}/tests/src ${CPP_BASE}/build ${CPP_BASE}/include ${CPP_BASE}/bmdscore ${EIGEN_DIR} ${NLOPT_DIR}/../include ${GSL_DIR})
 
 link_directories(${GSL_LIB_DIR} ${NLOPT_LIB_DIR})