Dev/serialization (#85)

* Injector serialization via pickle working * Remove cruft * Undo addition to DecaySignature * Remove printouts in DetectorModel serialization * Remove unnecessary cereal macros * Revert changes to link ordering * Remove comments * Don't need global FPIC now that it is handled with an INTERFACE target * Attempt to perform explicit template instantiation for interpolator templates * CMake fixes * Improve logic for finding cfitsio. Make an IMPORT target for cfitsio * Use lists for find_path * Search all paths in secondary searches * Remove printouts * Remove redundant paths for find_library * Link photospline with CFITSIO. Use generator expressions for -s and -stdlib=libc++ * Set policies for macos * Use photospline from icecube git repo. Update photospline and cereal * Remove printouts * Upgrade pybind11 * Use shared_ptr for compatibility of classes without a default constructor * Pickle weighter * Move external headers * pybind11 used in pickle serialization * Pickle serialization for dataclasses * Revert "Upgrade pybind11" This reverts commit add5a6a.
Harvard-Neutrino · Oct 23, 2024 · 82e4905 · 82e4905
1 parent f74be46
commit 82e4905
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Showing 80 changed files with 861 additions and 174 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -13,7 +13,7 @@
 	url = https://github.com/austinschneider/delabella.git
 [submodule "vendor/photospline"]
 	path = vendor/photospline
-	url = https://github.com/austinschneider/photospline.git
+	url = https://github.com/icecube/photospline.git
 [submodule "vendor/NamedType"]
 	path = vendor/NamedType
 	url = https://github.com/joboccara/NamedType.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,6 +2,10 @@ cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 cmake_policy(VERSION 3.20)
 
 if(${CMAKE_HOST_SYSTEM_NAME} MATCHES "Darwin")
+    set(CMAKE_POLICY_DEFAULT_CMP0042 NEW)
+    cmake_policy(SET CMP0042 NEW)
+    set(CMAKE_POLICY_DEFAULT_CMP0068 NEW)
+    cmake_policy(SET CMP0068 NEW)
     set(MACOSX TRUE)
 endif()
 
@@ -36,24 +40,50 @@ if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release")
 endif()
 
-# Create an interface library for SIREN compile options
-add_library(siren_compile_options INTERFACE)
+function(apply_siren_compile_options target)
+    # Check if the target is an INTERFACE target
+    get_target_property(target_type ${target} TYPE)
+    get_target_property(target_imported ${target} IMPORTED)
 
-# Specify the compile options
-target_compile_options(siren_compile_options INTERFACE
-    -O2
-    -Wall
-    -fPIC
-    $<$<CONFIG:Debug>:-g>
-    $<$<CONFIG:Debug>:-O0>
-    $<$<CONFIG:Release>:-O2>
-    $<$<CONFIG:Release>:-s>
-)
+    if("${target_type}" STREQUAL "INTERFACE_LIBRARY")
+        # Apply compile options to INTERFACE target
+        target_compile_options(${target} INTERFACE
+            -O2
+            -Wall
+            -fPIC
+            $<$<CONFIG:Debug>:-g>
+            $<$<CONFIG:Debug>:-O0>
+            $<$<CONFIG:Release>:-O2>
+            $<$<AND:$<COMPILE_LANG_AND_ID:CXX,GNU>,$<CONFIG:Release>>:-s>
+            $<$<COMPILE_LANG_AND_ID:CXX,Clang>:-stdlib=libc++>
+        )
+    elseif(target_imported)
+        # Apply compile options to non-INTERFACE target (PRIVATE or PUBLIC)
+        target_compile_options(${target} INTERFACE
+            -O2
+            -Wall
+            -fPIC
+            $<$<CONFIG:Debug>:-g>
+            $<$<CONFIG:Debug>:-O0>
+            $<$<CONFIG:Release>:-O2>
+            $<$<AND:$<COMPILE_LANG_AND_ID:CXX,GNU>,$<CONFIG:Release>>:-s>
+            $<$<COMPILE_LANG_AND_ID:CXX,Clang>:-stdlib=libc++>
+        )
+    else()
+        # Apply compile options to non-INTERFACE target (PRIVATE or PUBLIC)
+        target_compile_options(${target} PRIVATE
+            -O2
+            -Wall
+            -fPIC
+            $<$<CONFIG:Debug>:-g>
+            $<$<CONFIG:Debug>:-O0>
+            $<$<CONFIG:Release>:-O2>
+            $<$<AND:$<COMPILE_LANG_AND_ID:CXX,GNU>,$<CONFIG:Release>>:-s>
+            $<$<COMPILE_LANG_AND_ID:CXX,Clang>:-stdlib=libc++>
+        )
+    endif()
+endfunction()
 
-# Conditionally add -stdlib=libc++ for Clang
-if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
-    target_compile_options(siren_compile_options INTERFACE -stdlib=libc++)
-endif()
 
 # override install locations when building python extensions
 if(DEFINED SKBUILD_PLATLIB_DIR)
@@ -75,40 +105,44 @@ include(pybind11)
 # load project dependencies
 include(rk)
 if(TARGET rk_static)
-    target_link_libraries(rk_static INTERFACE siren_compile_options)
+    apply_siren_compile_options(rk_static)
 endif()
 if(TARGET rk_shared)
-    target_link_libraries(rk_shared INTERFACE siren_compile_options)
+    apply_siren_compile_options(rk_shared)
 endif()
 include(cereal)
 if(TARGET cereal)
-    target_link_libraries(cereal INTERFACE siren_compile_options)
+    apply_siren_compile_options(cereal)
 endif()
 include(delabella)
 if(TARGET delabella_static)
-    target_link_libraries(delabella_static INTERFACE siren_compile_options)
+    apply_siren_compile_options(delabella_static)
 endif()
 if(TARGET delabella_shared)
-    target_link_libraries(delabella_shared INTERFACE siren_compile_options)
+    apply_siren_compile_options(delabella_shared)
 endif()
 include(CFITSIO)
+if(TARGET CFITSIO)
+    apply_siren_compile_options(CFITSIO)
+endif()
 include(photospline)
 if(TARGET photospline)
-    target_link_libraries(photospline INTERFACE siren_compile_options)
+    apply_siren_compile_options(photospline)
+    target_link_libraries(photospline PUBLIC CFITSIO)
 endif()
 include(googletest)
 if(TARGET gtest)
-    target_link_libraries(gtest INTERFACE siren_compile_options)
+    apply_siren_compile_options(gtest)
 endif()
 if(TARGET gtest_main)
-    target_link_libraries(gtest_main INTERFACE siren_compile_options)
+    apply_siren_compile_options(gtest_main)
 endif()
 if(TARGET gmock)
-    target_link_libraries(gmock INTERFACE siren_compile_options)
+    apply_siren_compile_options(gmock)
 endif()
 include(NamedType)
 if(TARGET NamedType)
-    target_link_libraries(NamedType INTERFACE siren_compile_options)
+    apply_siren_compile_options(NamedType)
 endif()
 
 # load macros for googletest
@@ -128,7 +162,7 @@ add_subdirectory(projects/injection)
 # define the target library
 add_library(SIREN SHARED)
 set_property(TARGET SIREN PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(SIREN INTERFACE siren_compile_options)
+apply_siren_compile_options(SIREN)
 
 if(DEFINED MACOSX AND MACOSX)
 if(CMAKE_VERSION VERSION_LESS 3.13)
@@ -169,9 +203,6 @@ target_link_libraries(SIREN
 )
 endif()
 
-# Export siren_compile_options
-install(TARGETS siren_compile_options EXPORT ${PROJECT_NAME}Config)
-
 # define the install path normally or for python package
 if(DEFINED SKBUILD_PLATLIB_DIR)
     set_target_properties(SIREN PROPERTIES

diff --git a/cmake/Packages/CFITSIO.cmake b/cmake/Packages/CFITSIO.cmake
@@ -12,55 +12,105 @@
 #   CFITSIO_LDFLAGS                                                            #
 ################################################################################
 
-SET (CFITSIO_FIND_QUIETLY TRUE)
-SET (CFITSIO_FIND_REQUIRED TRUE)
-
-IF (NOT CFITSIO_FOUND)
-
-  # Search user environment for headers, then default paths; extract version
-  FIND_PATH (CFITSIO_INCLUDE_DIR fitsio.h
-    PATHS $ENV{CFITSIOROOT}/include
-    NO_DEFAULT_PATH)
-  FIND_PATH (CFITSIO_INCLUDE_DIR fitsio.h)
-  if(CFITSIO_INCLUDE_DIR)
-    GET_FILENAME_COMPONENT (CFITSIOROOT ${CFITSIO_INCLUDE_DIR} PATH)
-  else()
-    FIND_PATH (CFITSIO_INCLUDE_DIR cfitsio/fitsio.h
-      PATHS $ENV{CFITSIOROOT}/include
-      )
-    SET(CFITSIO_INCLUDE_DIR "${CFITSIO_INCLUDE_DIR}/cfitsio" CACHE PATH "Path to cfitsio headers" FORCE)
-  endif()
-
-  SET (CFITSIO_VERSION 0)
-  IF (CFITSIO_INCLUDE_DIR)
-    FILE (READ "${CFITSIO_INCLUDE_DIR}/fitsio.h" _cfitsio_VERSION)
-    STRING (REGEX REPLACE ".*define CFITSIO_VERSION ([0-9]+\\.[0-9]+).*" "\\1"
-            CFITSIO_VERSION "${_cfitsio_VERSION}")
-  ENDIF (CFITSIO_INCLUDE_DIR)
-
-  # Search user environment for libraries, then default paths
-  FIND_LIBRARY (CFITSIO_LIBRARIES NAMES cfitsio
-    PATHS $ENV{CFITSIOROOT}/lib
-    NO_DEFAULT_PATH)
-  FIND_LIBRARY (CFITSIO_LIBRARIES NAMES cfitsio)
-  GET_FILENAME_COMPONENT (CFITSIO_LIB_DIR ${CFITSIO_LIBRARIES} PATH)
-
-  # Set CFITSIO_FOUND and error out if cfitsio is not found
-  INCLUDE (FindPackageHandleStandardArgs)
-  FIND_PACKAGE_HANDLE_STANDARD_ARGS (CFITSIO
-    DEFAULT_MSG CFITSIO_LIBRARIES CFITSIO_INCLUDE_DIR)
-  ADD_DEFINITIONS ("-I${CFITSIO_INCLUDE_DIR}")
-
-  IF (CFITSIO_FOUND)
-    # Set flags and print a status message
-    MESSAGE (STATUS "CFITSIO version ${CFITSIO_VERSION} found:")
-
-    SET (CFITSIO_CPPFLAGS "-I${CFITSIO_INCLUDE_DIR}")
-    SET (CFITSIO_LDFLAGS "${CFITSIO_LIBRARIES}")
-
-    MESSAGE (STATUS "  * includes: ${CFITSIO_INCLUDE_DIR}")
-    MESSAGE (STATUS "  * libs:     ${CFITSIO_LIBRARIES}")
-  ENDIF (CFITSIO_FOUND)
-
-ENDIF (NOT CFITSIO_FOUND)
+include(FindPackageHandleStandardArgs)
+
+set(CFITSIO_FIND_QUIETLY TRUE)
+set(CFITSIO_FIND_REQUIRED TRUE)
+
+if (NOT CFITSIO_FOUND)
+    # Manually parse CPLUS_INCLUDE_PATH to add paths to search
+    if (DEFINED ENV{CPLUS_INCLUDE_PATH})
+        string(REPLACE ":" ";" CFITSIO_INCLUDE_SEARCH_PATH_LIST "$ENV{CPLUS_INCLUDE_PATH}")
+    else()
+        set(CFITSIO_INCLUDE_SEARCH_PATH_LIST "")
+    endif()
+
+    list(PREPEND CFITSIO_INCLUDE_SEARCH_PATH_LIST
+        $ENV{CFITSIOROOT}/include
+    )
+
+    # Search user environment for headers, then default paths; extract version
+    find_path(CFITSIO_INCLUDE_DIR fitsio.h
+        PATHS ${CFITSIO_INCLUDE_SEARCH_PATH_LIST}
+        NO_DEFAULT_PATH
+    )
+    if(NOT CFITSIO_INCLUDE_DIR)
+        unset(CFITSIO_INCLUDE_DIR)
+        find_path(CFITSIO_INCLUDE_DIR fitsio.h)
+    endif()
+
+    if(NOT CFITSIO_INCLUDE_DIR)
+        unset(CFITSIO_INCLUDE_DIR)
+        find_path(CFITSIO_INCLUDE_DIR cfitsio/fitsio.h
+            PATHS ${CFITSIO_INCLUDE_SEARCH_PATH_LIST}
+            NO_DEFAULT_PATH
+        )
+        if(CFITSIO_INCLUDE_DIR)
+            set(CFITSIO_INCLUDE_DIR "${CFITSIO_INCLUDE_DIR}/cfitsio" CACHE PATH "Path to cfitsio headers" FORCE)
+        endif()
+    endif()
+
+    if(NOT CFITSIO_INCLUDE_DIR)
+        unset(CFITSIO_INCLUDE_DIR)
+        find_path(CFITSIO_INCLUDE_DIR cfitsio/fitsio.h)
+        if(CFITSIO_INCLUDE_DIR)
+            set(CFITSIO_INCLUDE_DIR "${CFITSIO_INCLUDE_DIR}/cfitsio" CACHE PATH "Path to cfitsio headers" FORCE)
+        endif()
+    endif()
+
+    if (CFITSIO_INCLUDE_DIR AND EXISTS "${CFITSIO_INCLUDE_DIR}/fitsio.h")
+        get_filename_component(CFITSIOROOT ${CFITSIO_INCLUDE_DIR} PATH)
+        set(CFITSIO_VERSION 0)
+        file(STRINGS "${CFITSIO_INCLUDE_DIR}/fitsio.h" _cfitsio_VERSION REGEX "#define CFITSIO_VERSION[ \t]+([0-9]+\.[0-9]+)")
+        string(REGEX REPLACE ".*#define CFITSIO_VERSION[ \t]+([0-9]+\.[0-9]+).*" "\\1" CFITSIO_VERSION "${_cfitsio_VERSION}")
+    else()
+        set(CFITSIO_INCLUDE_DIR "CFITSIO_INCLUDE_DIR-NOTFOUND")
+    endif()
+
+    if (DEFINED ENV{LD_LIBRARY_PATH})
+        string(REPLACE ":" ";" CFITSIO_LIBRARY_SEARCH_PATH_LIST "$ENV{LD_LIBRARY_PATH}")
+    else()
+        set(CFITSIO_LIBRARY_SEARCH_PATH_LIST "")
+    endif()
+
+    # Search user environment for libraries, then default paths
+    find_library(CFITSIO_LIBRARIES cfitsio
+        PATHS ${CFITSIO_LIBRARY_SEARCH_PATH_LIST}
+        NO_DEFAULT_PATH
+    )
+
+    if(NOT CFITSIO_LIBRARIES)
+        find_library(CFITSIO_LIBRARIES NAMES cfitsio)
+    endif()
+
+    if (CFITSIO_LIBRARIES)
+        get_filename_component(CFITSIO_LIB_DIR ${CFITSIO_LIBRARIES} PATH)
+    else()
+        set(CFITSIO_LIBRARIES "CFITSIO_LIBRARIES-NOTFOUND")
+    endif()
+
+    # Set CFITSIO_FOUND and error out if cfitsio is not found
+    find_package_handle_standard_args(CFITSIO
+        REQUIRED_VARS CFITSIO_LIBRARIES CFITSIO_INCLUDE_DIR
+        VERSION_VAR CFITSIO_VERSION
+    )
+
+    if (CFITSIO_FOUND)
+        # Set flags and print a status message
+        message(STATUS "CFITSIO version ${CFITSIO_VERSION} found:")
+
+        set(CFITSIO_CPPFLAGS "-I${CFITSIO_INCLUDE_DIR}")
+        set(CFITSIO_LDFLAGS "${CFITSIO_LIBRARIES}")
+
+        message(STATUS "  * includes: ${CFITSIO_INCLUDE_DIR}")
+        message(STATUS "  * libs:     ${CFITSIO_LIBRARIES}")
+
+        add_library(CFITSIO SHARED IMPORTED)
+        target_include_directories(CFITSIO INTERFACE ${CFITSIO_INCLUDE_DIR})
+        set_target_properties(CFITSIO PROPERTIES
+            IMPORTED_LOCATION ${CFITSIO_LIBRARIES})
+    else()
+        message(WARNING "CFITSIO not found. Please ensure CFITSIO is installed and the environment variables CFITSIOROOT, CPLUS_INCLUDE_PATH, LIBRARY_PATH, and LD_LIBRARY_PATH are set correctly.")
+    endif()
+endif()
 
diff --git a/projects/dataclasses/CMakeLists.txt b/projects/dataclasses/CMakeLists.txt
@@ -17,14 +17,13 @@ target_include_directories(SIREN_dataclasses PUBLIC
 )
 
 target_link_libraries(SIREN_dataclasses
-    INTERFACE
-    siren_compile_options
     PUBLIC
     photospline
-    SIREN_serialization
     SIREN_utilities
+    SIREN_serialization
     SIREN_math
 )
+apply_siren_compile_options(SIREN_dataclasses)
 
 install(DIRECTORY "${PROJECT_SOURCE_DIR}/projects/dataclasses/public/"
     DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}

diff --git a/projects/dataclasses/private/pybindings/dataclasses.cxx b/projects/dataclasses/private/pybindings/dataclasses.cxx
@@ -8,6 +8,9 @@
 #include "../../public/SIREN/dataclasses/InteractionSignature.h"
 #include "../../public/SIREN/dataclasses/InteractionRecord.h"
 #include "../../public/SIREN/dataclasses/InteractionTree.h"
+#include "../../../serialization/public/SIREN/serialization/ByteString.h"
+
+#include "SIREN/dataclasses/serializable.h"
 
 #include <pybind11/pybind11.h>
 #include <pybind11/operators.h>
@@ -52,6 +55,10 @@ PYBIND11_MODULE(dataclasses, m) {
         .def_readwrite("length",&Particle::length)
         .def_readwrite("helicity",&Particle::helicity)
         .def("generate_id",&Particle::GenerateID)
+        .def(pybind11::pickle(
+            &(siren::serialization::pickle_save<Particle>),
+            &(siren::serialization::pickle_load<Particle>)
+        ))
         ;
 
     py::enum_<ParticleType>(m, "ParticleType", py::arithmetic())
@@ -67,6 +74,10 @@ PYBIND11_MODULE(dataclasses, m) {
         .def_readwrite("primary_type",&InteractionSignature::primary_type)
         .def_readwrite("target_type",&InteractionSignature::target_type)
         .def_readwrite("secondary_types",&InteractionSignature::secondary_types)
+        .def(pybind11::pickle(
+            &(siren::serialization::pickle_save<InteractionSignature>),
+            &(siren::serialization::pickle_load<InteractionSignature>)
+        ))
         ;
 
     py::class_<PrimaryDistributionRecord, std::shared_ptr<PrimaryDistributionRecord>>(m, "PrimaryDistributionRecord")
@@ -174,6 +185,10 @@ PYBIND11_MODULE(dataclasses, m) {
         .def_readwrite("secondary_momenta",&InteractionRecord::secondary_momenta)
         .def_readwrite("secondary_helicities",&InteractionRecord::secondary_helicities)
         .def_readwrite("interaction_parameters",&InteractionRecord::interaction_parameters)
+        .def(pybind11::pickle(
+            &(siren::serialization::pickle_save<InteractionRecord>),
+            &(siren::serialization::pickle_load<InteractionRecord>)
+        ))
         ;
 
     py::class_<InteractionTreeDatum, std::shared_ptr<InteractionTreeDatum>>(m, "InteractionTreeDatum")
@@ -182,13 +197,21 @@ PYBIND11_MODULE(dataclasses, m) {
         .def_readwrite("parent",&InteractionTreeDatum::parent)
         .def_readwrite("daughters",&InteractionTreeDatum::daughters)
         .def("depth",&InteractionTreeDatum::depth)
+        .def(pybind11::pickle(
+            &(siren::serialization::pickle_save<InteractionTreeDatum>),
+            &(siren::serialization::pickle_load<InteractionTreeDatum>)
+        ))
         ;
 
     py::class_<InteractionTree, std::shared_ptr<InteractionTree>>(m, "InteractionTree")
         .def(py::init<>())
         .def_readwrite("tree",&InteractionTree::tree)
         .def("add_entry",static_cast<std::shared_ptr<InteractionTreeDatum> (InteractionTree::*)(InteractionTreeDatum&,std::shared_ptr<InteractionTreeDatum>)>(&InteractionTree::add_entry))
         .def("add_entry",static_cast<std::shared_ptr<InteractionTreeDatum> (InteractionTree::*)(InteractionRecord&,std::shared_ptr<InteractionTreeDatum>)>(&InteractionTree::add_entry))
+        .def(pybind11::pickle(
+            &(siren::serialization::pickle_save<InteractionTree>),
+            &(siren::serialization::pickle_load<InteractionTree>)
+        ))
         ;
 
     m.def("SaveInteractionTrees",&SaveInteractionTrees);