Merge pull request #12 from noahares/feat_model_impr_pr

Model corrections, runtime improvements and highway heuristics
BenoitMorel · Oct 3, 2024 · 2fc2dd5 · 2fc2dd5
2 parents ab7bc8a + c7ce6bb
commit 2fc2dd5
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Showing 27 changed files with 1,678 additions and 1,704 deletions.
diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,7 @@
+# see https://clang.llvm.org/docs/ClangFormatStyleOptions.html
+---
+BasedOnStyle: LLVM
+Language: Cpp
+Standard: Cpp11
+
+UseTab: Never
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "ext/GeneRaxCore"]
 	path = ext/GeneRaxCore
-	url = https://github.com/BenoitMorel/GeneRaxCore.git
+	url = https://github.com/noahares/GeneRaxCore.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,6 +5,8 @@ project(AleRaxProject
 
 set(ALERAX_BUILD_AS_LIBRARY OFF CACHE BOOL "Build AleRax as shared library (instead of stand-alone executable)")
 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
 
 if(ALERAX_BUILD_AS_LIBRARY)

diff --git a/ext/GeneRaxCore b/ext/GeneRaxCore
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,6 +1,7 @@
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wextra")
 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 macro(add_program program_name program_sources)
   if (ALERAX_BUILD_AS_LIBRARY)
@@ -9,7 +10,7 @@ macro(add_program program_name program_sources)
     add_executable(${program_name} ${program_sources})
   endif()
   target_sources(${program_name} PRIVATE ${program_sources})
-  target_link_libraries(${program_name} 
+  target_link_libraries(${program_name}
     PRIVATE
     generaxcore
     ${CORAX_LIB_TARGET}
@@ -25,11 +26,11 @@ macro(add_program program_name program_sources)
     PROPERTIES
     RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
     )
-  set_target_properties(${program_name} 
+  set_target_properties(${program_name}
     PROPERTIES
     COMPILE_FLAGS "-g ${MPI_COMPILE_FLAGS}"
     )
-  set_target_properties(${program_name} 
+  set_target_properties(${program_name}
     PROPERTIES
     LINK_FLAGS "${MPI_LINK_FLAGS}"
     )
@@ -45,7 +46,7 @@ macro(add_program_corax program_name program_sources)
   else()
     add_executable(${program_name} ${program_sources})
   endif()
-  target_link_libraries(${program_name} 
+  target_link_libraries(${program_name}
     generaxcore
     ${CORAX_LIB_TARGET}
     ${MPI_LIBRARIES}
@@ -60,11 +61,11 @@ macro(add_program_corax program_name program_sources)
     PROPERTIES
     RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
     )
-  set_target_properties(${program_name} 
+  set_target_properties(${program_name}
     PROPERTIES
     COMPILE_FLAGS "-g ${MPI_COMPILE_FLAGS}"
     )
-  set_target_properties(${program_name} 
+  set_target_properties(${program_name}
     PROPERTIES
     LINK_FLAGS "${MPI_LINK_FLAGS}"
     )
@@ -78,4 +79,3 @@ endmacro()
 
 add_subdirectory(tools)
 add_subdirectory(ale)
-
+1 −1		ext/coraxlib
+1 −2		src/CMakeLists.txt
+7 −3		src/IO/HighwayCandidateParser.hpp
+4 −3		src/IO/ReconciliationWriter.cpp
+2 −2		src/maths/Parameters.hpp
+10 −4		src/optimizers/DTLOptimizer.cpp
+9 −1		src/optimizers/DTLOptimizer.hpp
+2 −1		src/routines/Routines.cpp
+13 −1		src/util/Scenario.cpp
+2 −0		src/util/Scenario.hpp
+2 −1		src/util/enums.hpp