Merge/alexwenym (#29)

* ATALS, QOL changes, and Column Depth fixes (#27)

* atlas notebook, added some pybindings

* updates to SNe Ranged injection

* incremental changes for atlas injection, columndepth debug ongoing

* added some pybindings to help debug classes Path and ColumnDepthPositionDistribution

* Fix column depth unit conversions. Fix unsigned integer overflow in bounds clipping. Fix spacing.

* Special case for constructing 180deg rotation Quaternion for a rotation between opposing directions.

* Include what you use

* Convert from detector coordinates to earth coordinates before checking bounds

* Removed extra files, some may need to be added to resources later

* TreeWeighter constructor w/o secondary processes

* Delete Doxyfile

Removing unnecessary file

---------

Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Philip Weigel <[email protected]>

* Add Placement pybindings

* Add Quaternion python bindings

* EarthModel pybindings

* Default constructor for EarthSector. Fix name collision for static and non-static methods in EarthModel

* Move detector pybindings into separate files. Add DensityDistribution pybindings

* pybindings for Axis1D and Distribution1D

* pybindings for CartesianAxis1D

* Axis1D has pure virtual functions

* Add Axis1D and Distribution1D subclasses

* Polynomial and Exponential cartesian axis distributions

* Remove non-existent comparison operators

* Add pybindings for ConstantDensityDistribution

* Fix pybindings name for ConstantDistribution1D

* Add EarthSector python printout

* MaterialModel bindings. Remove unnecessary LeptonDepthFunction method

* MaterialModel pybindings

* DummyCrossSection

* Sketch helper class for CrossSection pybindings

* Reindent

* CrossSection pybindings

* Re-organize crosssections pybindings

* pybindings for DummyCrossSection

* More realistic total cross section for DummyCrossSection

* Add interaction probability to pybindings

* Fixed == and != operators to play well with pybind11's execute_cast

* Update build_wheels.yml

* starting to add HNL classes

* Use a specific python version if specified

* Remove parts of interface that depend on rk

* Explicitly label rk static lib. Export cmake project for rk

* Use rk_static in testing. Use photosplines internal install directives so we can export it as a cmake project.

* Incude cassert (previously included via rk)

* Export cmake project. Specify public asnd private link libs. Remove unneeded dependencies. Guard include dirs at install

* Install cereal so other libraries can use it

* Install delabella so other libraries can use it

* Use a single export name for rk

* Use a single export name for delabella

* Move around includes

* Rearranging includes to enforce "include what you use"

* Move around includes to comply with IWYU

* Delete resources/DipoleInjection/inject_HNLs_CCM.ipynb

* Delete resources/DipoleInjection/Makefile

* Rename Makefile_original to Makefile

---------

Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Alex Wen <[email protected]>
Co-authored-by: Philip Weigel <[email protected]>
Co-authored-by: Austin William Schneider <[email protected]>
Co-authored-by: Nicholas Kamp <[email protected]>

.github/workflows/build_wheels.yml

@@ -10,6 +10,7 @@ jobs:
       matrix:
         #os: [ubuntu-20.04, windows-2019, macos-11]
         os: [ubuntu-20.04, macos-11]
+        arch: [x86_64, auto32, auto64, aarch64, ppc64le, s390x, arm64]
 
     steps:
       - name: Checkout LeptonInjector

CMakeLists.txt

@@ -58,26 +58,8 @@ else()
 endif()
 
 # load python and pybind11
+include(Python)
 include(pybind11)
-if(CMAKE_VERSION VERSION_LESS 3.12.0)
-    if(Python_ROOT_DIR)
-        MESSAGE(WARNING "Python_ROOT_DIR is set but will be ignored by this version of CMake; set PYTHON_EXECUTABLE instead")
-	endif()
-	find_package(PythonInterp)
-	find_package(PythonLibs)
-	set(PYTHON_FOUND PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
-else()
-    if(PYTHON_EXECUTABLE)
-        MESSAGE(WARNING "PYTHON_EXECUTABLE is set but will be ignored by this version of CMake; set Python_ROOT_DIR instead")
-	endif()
-    find_package(Python COMPONENTS Interpreter Development)
-    set(PYTHON_FOUND Python_Interpreter_FOUND AND Python_Development_FOUND)
-    set(PYTHON_EXECUTABLE "${Python_EXECUTABLE}")
-	set(PYTHON_INCLUDE_DIRS "${Python_INCLUDE_DIRS}")
-	set(PYTHON_LIBRARIES "${Python_LIBRARIES}")
-	set(PYTHON_VERSION_MAJOR "${Python_VERSION_MAJOR}")
-	set(PYTHON_VERSION_MINOR "${Python_VERSION_MINOR}")
-endif()
 
 # load project dependencies
 include(rk)
@@ -105,33 +87,35 @@ add_library(LeptonInjector SHARED)
 set_property(TARGET LeptonInjector PROPERTY POSITION_INDEPENDENT_CODE ON)
 if(${MACOSX})
 target_link_libraries(LeptonInjector
-    LI_utilities
-    LI_serialization
-    LI_math
-    LI_dataclasses
-    LI_geometry
-    LI_detector
-    LI_crosssections
-    LI_distributions
-    LI_injection
-    rk
-    delabella
+    PRIVATE
+    PUBLIC
+        delabella_shared
+        photospline
+        LI_utilities
+        LI_serialization
+        LI_math
+        LI_dataclasses
+        LI_geometry
+        LI_detector
+        LI_crosssections
+        LI_distributions
+        LI_injection
 )
 else()
 target_link_libraries(LeptonInjector
-    LI_utilities
-    LI_serialization
-    LI_math
-    LI_dataclasses
-    LI_geometry
-    LI_detector
-    LI_crosssections
-    LI_distributions
-    LI_injection
-    -Wl,--whole-archive
-    rk
-    delabella
-    -Wl,--no-whole-archive
+    PRIVATE
+    PUBLIC
+        photospline
+        delabella_shared
+        LI_utilities
+        LI_serialization
+        LI_math
+        LI_dataclasses
+        LI_geometry
+        LI_detector
+        LI_crosssections
+        LI_distributions
+        LI_injection
 )
 endif()
 
@@ -144,15 +128,48 @@ if(DEFINED SKBUILD)
         message(STATUS "Setting LeptonInjector install lib dir to: ${CI_INSTALL_PREFIX}/lib")
         message(STATUS "Setting LeptonInjector install include dir to: ${CI_INSTALL_PREFIX}/include")
         install(TARGETS LeptonInjector
+            delabella_shared
+            LI_utilities
+            LI_serialization
+            LI_math
+            LI_dataclasses
+            LI_geometry
+            LI_detector
+            LI_crosssections
+            LI_distributions
+            LI_injection
+            EXPORT ${PROJECT_NAME}Config
             LIBRARY DESTINATION "${CI_INSTALL_PREFIX}/lib"
             PUBLIC_HEADER DESTINATION "${CI_INSTALL_PREFIX}/include")
     else()
         install(TARGETS LeptonInjector
+            delabella_shared
+            LI_utilities
+            LI_serialization
+            LI_math
+            LI_dataclasses
+            LI_geometry
+            LI_detector
+            LI_crosssections
+            LI_distributions
+            LI_injection
+            EXPORT ${PROJECT_NAME}Config
             LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector.libs
             PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
     endif()
 else()
     install(TARGETS LeptonInjector
+        delabella_shared
+        LI_utilities
+        LI_serialization
+        LI_math
+        LI_dataclasses
+        LI_geometry
+        LI_detector
+        LI_crosssections
+        LI_distributions
+        LI_injection
+        EXPORT ${PROJECT_NAME}Config
         LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
         PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 endif()
@@ -201,9 +218,30 @@ if(DEFINED SKBUILD)
         LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector)
     install(TARGETS injection
         LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector)
-    install(FILES ${PROJECT_SOURCE_DIR}/python/__init__.py DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector)
+    install(FILES ${PROJECT_SOURCE_DIR}/python/__init__.py
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector)
 endif()
 
+# Export targets for use in downstream CMake projects
+# -----------------------------------------------------------------------------
+include(CMakePackageConfigHelpers)
+# Make importable from build directory
+write_basic_package_version_file(
+  "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY AnyNewerVersion
+)
+export(EXPORT ${PROJECT_NAME}Config FILE ${PROJECT_NAME}Config.cmake)
+
+# Make importable from install location
+set(_config_dir share/${PROJECT_NAME}/cmake)
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
+  DESTINATION ${_config_dir}
+)
+install(EXPORT ${PROJECT_NAME}Config
+  DESTINATION ${_config_dir}
+)
+
 MESSAGE("")
 MESSAGE("Done!")
 MESSAGE("Run `make` then `make install`")

cmake/Packages/Python.cmake

@@ -2,14 +2,23 @@ IF(CMAKE_VERSION VERSION_LESS 3.12.0)
     IF(Python_ROOT_DIR)
         MESSAGE(WARNING "Python_ROOT_DIR is set but will be ignored by this version of CMake; set PYTHON_EXECUTABLE instead")
     ENDIF(Python_ROOT_DIR)
-    find_package(PythonInterp)
-    find_package(PythonLibs)
+    IF(PYTHON_VERSION)
+        find_package(PythonInterp ${PYTHON_VERSION})
+        find_package(PythonLibs ${PYTHON_VERSION})
+    ELSE(PYTHON_VERSION)
+      find_package(PythonInterp)
+      find_package(PythonLibs)
+    ENDIF(PYTHON_VERSION)
     set(PYTHON_FOUND PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
 ELSE()
     IF(PYTHON_EXECUTABLE)
         MESSAGE(WARNING "PYTHON_EXECUTABLE is set but will be ignored by this version of CMake; set Python_ROOT_DIR instead")
     ENDIF(PYTHON_EXECUTABLE)
-    FIND_PACKAGE(Python COMPONENTS Interpreter Development)
+    IF(PYTHON_VERSION)
+      FIND_PACKAGE(Python ${PYTHON_VERSION} COMPONENTS Interpreter Development)
+    ELSE(PYTHON_VERSION)
+      FIND_PACKAGE(Python COMPONENTS Interpreter Development)
+    ENDIF(PYTHON_VERSION)
     SET(PYTHON_FOUND "${Python_FOUND}")
     SET(PYTHON_EXECUTABLE "${Python_EXECUTABLE}")
     SET(PYTHON_INCLUDE_DIRS "${Python_INCLUDE_DIRS}")

cmake/Packages/cereal.cmake

@@ -22,5 +22,5 @@ endif()
 set(JUST_INSTALL_CEREAL ON CACHE INTERNAL "Cereal just install library.")
 set(SKIP_PORTABILITY_TEST ON CACHE INTERNAL "Skip cereal portability tests.")
 set(SKIP_PERFORMANCE_COMPARISON ON CACHE INTERNAL "Skip cereal performance comparison.")
-add_subdirectory("${PROJECT_SOURCE_DIR}/vendor/cereal" "extern/cereal" EXCLUDE_FROM_ALL)
+add_subdirectory("${PROJECT_SOURCE_DIR}/vendor/cereal" "extern/cereal")
 include_directories("${PROJECT_SOURCE_DIR}/vendor/cereal/include")

cmake/Packages/delabella.cmake

@@ -19,4 +19,14 @@ if(NOT EXISTS "${PROJECT_SOURCE_DIR}/vendor/delabella/CMakeLists.txt")
     message(FATAL_ERROR "The delabella submodule was not downloaded! GIT_SUBMODULE was turned off or failed. Please update submodules and try again.")
 endif()
 
-add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/delabella EXCLUDE_FROM_ALL)
+add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/delabella)
+#add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/delabella)
+#install(TARGETS delabella_shared
+#    ARCHIVE DESTINATION lib)
+#set(_config_dir share/delabella/cmake)
+#install(FILES "${CMAKE_CURRENT_BINARY_DIR}/delabellaConfigVersion.cmake"
+#  DESTINATION ${_config_dir}
+#)
+#install(EXPORT delabellaConfig
+#  DESTINATION ${_config_dir}
+#)

cmake/Packages/photospline.cmake

@@ -19,7 +19,8 @@ if(NOT EXISTS "${PROJECT_SOURCE_DIR}/vendor/photospline/CMakeLists.txt")
     message(FATAL_ERROR "The photospline submodule was not downloaded! GIT_SUBMODULE was turned off or failed. Please update submodules and try again.")
 endif()
 
-add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/photospline EXCLUDE_FROM_ALL)
+#add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/photospline EXCLUDE_FROM_ALL)
+add_subdirectory(${PROJECT_SOURCE_DIR}/vendor/photospline)
 if(DEFINED SKBUILD)
     if(${CIBUILDWHEEL})
         message(STATUS "Setting photospline install lib dir to: ${CI_INSTALL_PREFIX}/lib")
@@ -42,6 +43,6 @@ if(DEFINED SKBUILD)
     #    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/leptoninjector.libs
     #    PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 else()
-    install(TARGETS photospline DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    #install(TARGETS photospline DESTINATION ${CMAKE_INSTALL_LIBDIR})
     #install(TARGETS spglam DESTINATION ${CMAKE_INSTALL_LIBDIR})
 endif()

cmake/testing.cmake

@@ -13,7 +13,7 @@ set_target_properties(gmock_main PROPERTIES FOLDER extern)
 macro(package_add_test TESTNAME)
 	add_executable(${TESTNAME} ${ARGN})
     target_link_libraries(${TESTNAME} gtest gmock gtest_main LeptonInjector)
-    add_dependencies(${TESTNAME} rk)
+    add_dependencies(${TESTNAME} rk_static)
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} WORKING_DIRECTORY ${PROJECT_BINARY_DIR})
 	set_target_properties(${TESTNAME} PROPERTIES FOLDER tests)
 endmacro()

projects/crosssections/CMakeLists.txt

@@ -7,28 +7,28 @@ LIST (APPEND crosssections_SOURCES
     ${PROJECT_SOURCE_DIR}/projects/crosssections/private/DipoleFromTable.cxx
     ${PROJECT_SOURCE_DIR}/projects/crosssections/private/NeutrissimoDecay.cxx
     ${PROJECT_SOURCE_DIR}/projects/crosssections/private/DISFromSpline.cxx
+    ${PROJECT_SOURCE_DIR}/projects/crosssections/private/HNLFromSpline.cxx
     ${PROJECT_SOURCE_DIR}/projects/crosssections/private/ElasticScattering.cxx
+    ${PROJECT_SOURCE_DIR}/projects/crosssections/private/DummyCrossSection.cxx
 )
 add_library(LI_crosssections OBJECT ${crosssections_SOURCES})
 set_property(TARGET LI_crosssections PROPERTY POSITION_INDEPENDENT_CODE ON)
 target_include_directories(LI_crosssections PUBLIC
-    ${PROJECT_SOURCE_DIR}/projects/crosssections/public/
+    $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/projects/crosssections/public/>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/LeptonInjector/crosssections/>
 )
-add_dependencies(LI_crosssections rk)
-add_dependencies(LI_crosssections LI_serialization LI_utilities LI_math LI_dataclasses LI_detector)
 
-target_link_libraries(LI_crosssections photospline)
-target_link_libraries(LI_crosssections rk)
-
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/vendor/rk/include)
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/projects/serialization/public/)
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/projects/utilities/public/)
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/projects/math/public/)
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/projects/detector/public/)
-target_include_directories(LI_crosssections PUBLIC ${PROJECT_SOURCE_DIR}/projects/dataclasses/public/)
-
-install(TARGETS LI_crosssections
-    PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+target_link_libraries(LI_crosssections
+    PRIVATE
+        $<BUILD_INTERFACE:rk_static>
+    PUBLIC
+        photospline
+        LI_serialization
+        LI_utilities
+        LI_math
+        LI_dataclasses
+        LI_detector
+)
 
 install(DIRECTORY "${PROJECT_SOURCE_DIR}/projects/crosssections/public/"
     DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
@@ -42,7 +42,7 @@ package_add_test(UnitTest_DipoleFromTable ${PROJECT_SOURCE_DIR}/projects/crossse
 #package_add_test(UnitTest_ElasticScattering ${PROJECT_SOURCE_DIR}/projects/crosssections/private/test/ElasticScattering_TEST.cxx)
 
 pybind11_add_module(crosssections ${PROJECT_SOURCE_DIR}/projects/crosssections/private/pybindings/crosssections.cxx)
-target_link_libraries(crosssections PRIVATE LeptonInjector photospline rk)
+target_link_libraries(crosssections PRIVATE LeptonInjector photospline rk_static)
 if(DEFINED SKBUILD)
 set_target_properties(crosssections PROPERTIES
         BUILD_WITH_INSTALL_RPATH FALSE

projects/crosssections/private/CrossSectionCollection.cxx

@@ -1,14 +1,18 @@
-#include <map>
-#include <set>
-#include <vector>
-#include <string>
-#include <memory>
-
-#include "LeptonInjector/dataclasses/Particle.h"
-
-#include "LeptonInjector/crosssections/CrossSection.h"
 #include "LeptonInjector/crosssections/CrossSectionCollection.h"
 
+#include <map>                                                // for map
+#include <set>                                                // for operator==
+#include <tuple>                                              // for tie
+#include <limits>                                             // for numeric...
+#include <vector>                                             // for vector
+#include <utility>                                            // for pair
+
+#include "LeptonInjector/crosssections/CrossSection.h"        // for CrossSe...
+#include "LeptonInjector/crosssections/Decay.h"               // for Decay
+#include "LeptonInjector/dataclasses/InteractionRecord.h"     // for Interac...
+#include "LeptonInjector/dataclasses/InteractionSignature.h"  // for Interac...
+#include "LeptonInjector/dataclasses/Particle.h"              // for Particle
+
 namespace LI {
 namespace crosssections {
 

projects/crosssections/private/DISFromSpline.cxx

@@ -1,22 +1,27 @@
-#include <map>
-#include <set>
-#include <vector>
-#include <string>
-#include <memory>
-
-#include <rk/rk.hh>
-#include <rk/geom3.hh>
-
-#include <photospline/splinetable.h>
-#include <photospline/cinter/splinetable.h>
-
-#include "LeptonInjector/dataclasses/Particle.h"
-
-#include "LeptonInjector/utilities/Random.h"
-
-#include "LeptonInjector/crosssections/CrossSection.h"
 #include "LeptonInjector/crosssections/DISFromSpline.h"
 
+#include <map>                                             // for map, opera...
+#include <set>                                             // for set, opera...
+#include <array>                                           // for array
+#include <cmath>                                           // for pow, log10
+#include <tuple>                                           // for tie, opera...
+#include <memory>                                          // for allocator
+#include <string>                                          // for basic_string
+#include <vector>                                          // for vector
+#include <assert.h>                                        // for assert
+#include <stddef.h>                                        // for size_t
+
+#include <rk/rk.hh>                                        // for P4, Boost
+#include <rk/geom3.hh>                                     // for Vector3
+
+#include <photospline/splinetable.h>                       // for splinetable
+//#include <photospline/cinter/splinetable.h>
+
+#include "LeptonInjector/crosssections/CrossSection.h"     // for CrossSection
+#include "LeptonInjector/dataclasses/InteractionRecord.h"  // for Interactio...
+#include "LeptonInjector/dataclasses/Particle.h"           // for Particle
+#include "LeptonInjector/utilities/Random.h"               // for LI_random
+
 namespace LI {
 namespace crosssections {
 

projects/crosssections/private/Decay.cxx

@@ -1,7 +1,12 @@
 #include "LeptonInjector/crosssections/Decay.h"
-#include "LeptonInjector/utilities/Constants.h"
 
-#include <rk/rk.hh>
+#include <array>                                           // for array
+
+#include <rk/rk.hh>                                        // for P4
+#include <rk/geom3.hh>                                     // for Vector3
+
+#include "LeptonInjector/dataclasses/InteractionRecord.h"
+#include "LeptonInjector/utilities/Constants.h"
 
 namespace LI {
 namespace crosssections {