Harvard-Neutrino · austinschneider · Jun 3, 2024 · Mar 28, 2024 · Apr 12, 2024 · Apr 25, 2024
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -3,60 +3,73 @@ name: Build
 on: [pull_request]
 
 jobs:
-  build_wheels_linux:
+  build_wheels_macos:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
-        arch: [x86_64, i686, aarch64, ppc64le, s390x]
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [macos-13, macos-14]
+        py: [cp38, cp39, cp311, cp312]
 
     steps:
-      - name: Checkout SIREN
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v3
         with:
-          python-version: '3.9'  # update once build dependencies are available
+          platforms: all
 
       - name: Build wheels
-        uses: pypa/[email protected]
-
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
+        uses: pypa/[email protected]
+        env:
+          # configure cibuildwheel to build native archs ('auto'), and some
+          # emulated ones
+          CIBW_BUILD: ${{ matrix.py }}-*
+          CIBW_ARCHS_LINUX: auto
 
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
-  build_wheels_macos:
+
+  build_wheels_linux:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-11]
-        # arch: [x86_64, arm64]
-        arch: [x86_64]
+        os: [ubuntu-latest]
+        py: [cp38, cp39, cp311, cp312]
+        image: [manylinux, musllinux]
+        arch: [x86_64, i686, aarch64, ppc64le, s390x]
 
     steps:
-      - name: Checkout SIREN
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v3
         with:
-          python-version: '3.9'  # update once build dependencies are available
+          platforms: all
 
       - name: Build wheels
-        uses: pypa/[email protected]
-
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
+        uses: pypa/[email protected]
+        env:
+          # configure cibuildwheel to build native archs ('auto'), and some
+          # emulated ones
+          CIBW_BUILD: ${{ matrix.py }}-${{ matrix.image }}_${{ matrix.arch }}
+          CIBW_ARCHS: all
 
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
+  merge:
+    runs-on: ubuntu-latest
+    needs: [build_wheels_macos, build_wheels_linux]
+    steps:
+      - name: Merge Artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          delete-merged: true
diff --git a/projects/dataclasses/private/InteractionTree.cxx b/projects/dataclasses/private/InteractionTree.cxx
@@ -23,7 +23,7 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(std::shared_ptr
         datum->parent = parent;
         parent->daughters.push_back(datum);
     }
-    tree.insert(datum);
+    tree.push_back(datum);
     return datum;
 }
 
@@ -34,7 +34,7 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(InteractionTree
         _datum->parent = parent;
         parent->daughters.push_back(_datum);
     }
-    tree.insert(_datum);
+    tree.push_back(_datum);
     return _datum;
 }
 
@@ -45,9 +45,23 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(InteractionReco
         datum->parent = parent;
         parent->daughters.push_back(datum);
     }
-    tree.insert(datum);
+    tree.push_back(datum);
     return datum;
 }
 
+void SaveInteractionTrees(std::vector<std::shared_ptr<InteractionTree>>& trees, std::string const & filename) {
+    std::ofstream os(filename+".siren_events", std::ios::binary);
+    ::cereal::BinaryOutputArchive archive(os);
+    archive(trees);
+}
+
+std::vector<std::shared_ptr<InteractionTree>> LoadInteractionTrees(std::string const & filename) {
+    std::ifstream is(filename+".siren_events", std::ios::binary);
+    ::cereal::BinaryInputArchive archive(is);
+    std::vector<std::shared_ptr<InteractionTree>> trees;
+    archive(trees);
+    return trees;
+}
+
 } // namespace dataclasses
 } // namespace siren
diff --git a/projects/dataclasses/private/pybindings/dataclasses.cxx b/projects/dataclasses/private/pybindings/dataclasses.cxx
@@ -148,4 +148,7 @@ PYBIND11_MODULE(dataclasses,m) {
           .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));
 
+  m.def("SaveInteractionTrees",&SaveInteractionTrees);
+  m.def("LoadInteractionTrees",&LoadInteractionTrees,pybind11::return_value_policy::reference);
+
 }
diff --git a/projects/dataclasses/private/test/InteractionTree_TEST.cxx b/projects/dataclasses/private/test/InteractionTree_TEST.cxx
@@ -42,7 +42,7 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(std::shared_ptr
         datum->parent = parent;
         parent->daughters.push_back(datum);
     }
-    tree.insert(datum);
+    tree.push_back(datum);
     return datum;
 }
 
@@ -53,7 +53,7 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(InteractionTree
         _datum->parent = parent;
         parent->daughters.push_back(_datum);
     }
-    tree.insert(_datum);
+    tree.push_back(_datum);
     return _datum;
 }
 
@@ -64,7 +64,7 @@ std::shared_ptr<InteractionTreeDatum> InteractionTree::add_entry(InteractionReco
         datum->parent = parent;
         parent->daughters.push_back(datum);
     }
-    tree.insert(datum);
+    tree.push_back(datum);
     return datum;
 }
 

diff --git a/projects/dataclasses/public/SIREN/dataclasses/InteractionRecord.h b/projects/dataclasses/public/SIREN/dataclasses/InteractionRecord.h
@@ -12,6 +12,7 @@
 #include <cereal/archives/json.hpp>
 #include <cereal/archives/binary.hpp>
 #include <cereal/types/vector.hpp>
+#include <cereal/types/map.hpp>
 #include <cereal/types/array.hpp>
 #include <cereal/types/polymorphic.hpp>
 #include <cereal/types/base_class.hpp>

diff --git a/projects/dataclasses/public/SIREN/dataclasses/InteractionTree.h b/projects/dataclasses/public/SIREN/dataclasses/InteractionTree.h
@@ -10,6 +10,7 @@
 #include <cstdint>                                         // for uint32_t
 #include <stddef.h>                                        // for NULL
 #include <stdexcept>                                       // for runtime_error
+#include <fstream>                                         // for if/ofstream
 
 #include <cereal/cereal.hpp>
 #include <cereal/archives/json.hpp>
@@ -24,6 +25,7 @@ namespace siren {
 namespace dataclasses {
 
 struct InteractionTreeDatum {
+  InteractionTreeDatum() {}
   InteractionTreeDatum(dataclasses::InteractionRecord& record) : record(record) {}
   dataclasses::InteractionRecord record;
   std::shared_ptr<dataclasses::InteractionTreeDatum> parent = NULL;
@@ -42,7 +44,7 @@ struct InteractionTreeDatum {
 };
 
 struct InteractionTree {
-  std::set<std::shared_ptr<dataclasses::InteractionTreeDatum>> tree;
+  std::vector<std::shared_ptr<dataclasses::InteractionTreeDatum>> tree;
   std::shared_ptr<InteractionTreeDatum> add_entry(std::shared_ptr<dataclasses::InteractionTreeDatum> datum,
                                                   std::shared_ptr<dataclasses::InteractionTreeDatum> parent = NULL);
   std::shared_ptr<InteractionTreeDatum> add_entry(dataclasses::InteractionTreeDatum& datum,
@@ -59,8 +61,14 @@ struct InteractionTree {
   };
 };
 
+void SaveInteractionTrees(std::vector<std::shared_ptr<InteractionTree>>& trees, std::string const & filename);
+std::vector<std::shared_ptr<InteractionTree>> LoadInteractionTrees(std::string const & filename);
+
 } // namespace dataclasses
 } // namespace siren
 
+CEREAL_CLASS_VERSION(siren::dataclasses::InteractionTreeDatum, 0);
+CEREAL_CLASS_VERSION(siren::dataclasses::InteractionTree, 0);
+
 #endif // SIREN_InteractionTree_H
 
diff --git a/projects/dataclasses/public/SIREN/dataclasses/ParticleID.h b/projects/dataclasses/public/SIREN/dataclasses/ParticleID.h
@@ -4,6 +4,7 @@
 #include <cstdint>                                      // for uint32_t
 #include <ostream>                                      // for ostream
 #include <stdexcept>                                    // for runtime_error
+#include <sstream>
 
 #include <cereal/cereal.hpp>
 #include <cereal/archives/json.hpp>

diff --git a/projects/detector/public/SIREN/detector/MaterialModel.h b/projects/detector/public/SIREN/detector/MaterialModel.h
@@ -98,6 +98,7 @@ class MaterialModel {
             archive(cereal::make_nvp("MaterialNames", material_names_));
             archive(cereal::make_nvp("MaterialIDs", material_ids_));
             archive(cereal::make_nvp("MaterialComponents", material_components_));
+            archive(cereal::make_nvp("MaterialComponentsByID", material_components_by_id_));
             archive(cereal::make_nvp("MaterialRadiationLength", material_radiation_length_));
             archive(cereal::make_nvp("ComponentRadiationLength", component_radiation_length_));
         } else {

diff --git a/projects/distributions/CMakeLists.txt b/projects/distributions/CMakeLists.txt
@@ -44,6 +44,7 @@ target_include_directories(SIREN_distributions PUBLIC
 target_link_libraries(SIREN_distributions
     PRIVATE
         $<BUILD_INTERFACE:rk_static>
+        pybind11::embed
     PUBLIC
         photospline
         SIREN_serialization

diff --git a/projects/distributions/private/primary/energy/TabulatedFluxDistribution.cxx b/projects/distributions/private/primary/energy/TabulatedFluxDistribution.cxx
@@ -292,9 +292,9 @@ bool TabulatedFluxDistribution::equal(WeightableDistribution const & other) cons
         return false;
     else
         return
-            std::tie(energyMin, energyMax, fluxTableFilename)
+            std::tie(energyMin, energyMax, fluxTable)
             ==
-            std::tie(x->energyMin, x->energyMax, x->fluxTableFilename);
+            std::tie(x->energyMin, x->energyMax, x->fluxTable);
 }
 
 bool TabulatedFluxDistribution::less(WeightableDistribution const & other) const {

diff --git a/projects/distributions/public/SIREN/distributions/primary/energy/TabulatedFluxDistribution.h b/projects/distributions/public/SIREN/distributions/primary/energy/TabulatedFluxDistribution.h
@@ -84,7 +84,9 @@ friend cereal::access;
             archive(::cereal::make_nvp("EnergyMax", energyMax));
             archive(::cereal::make_nvp("FluxTable", fluxTable));
             archive(cereal::virtual_base_class<PrimaryEnergyDistribution>(this));
+            bounds_set = true;
             ComputeIntegral();
+            ComputeCDF();
         } else {
             throw std::runtime_error("TabulatedFluxDistribution only supports version <= 0!");
         }

diff --git a/projects/distributions/public/SIREN/distributions/primary/vertex/DepthFunction.h b/projects/distributions/public/SIREN/distributions/primary/vertex/DepthFunction.h
@@ -49,5 +49,6 @@ friend cereal::access;
 } // namespace siren
 
 CEREAL_CLASS_VERSION(siren::distributions::DepthFunction, 0);
+CEREAL_REGISTER_TYPE(siren::distributions::DepthFunction);
 
 #endif // SIREN_DepthFunction_H
diff --git a/projects/distributions/public/SIREN/distributions/primary/vertex/LeptonDepthFunction.h b/projects/distributions/public/SIREN/distributions/primary/vertex/LeptonDepthFunction.h
@@ -48,28 +48,28 @@ friend cereal::access;
     template<typename Archive>
     void save(Archive & archive, std::uint32_t const version) const {
         if(version == 0) {
-        } else {
             archive(::cereal::make_nvp("MuAlpha", mu_alpha));
             archive(::cereal::make_nvp("MuBeta", mu_beta));
             archive(::cereal::make_nvp("TauAlpha", tau_alpha));
             archive(::cereal::make_nvp("TauBeta", tau_beta));
             archive(::cereal::make_nvp("Scale", scale));
             archive(::cereal::make_nvp("MaxDepth", max_depth));
             archive(::cereal::make_nvp("TauPrimaries", tau_primaries));
+        } else {
             throw std::runtime_error("LeptonDepthFunction only supports version <= 0!");
         }
     }
     template<typename Archive>
     void load(Archive & archive, std::uint32_t const version) {
         if(version == 0) {
-        } else {
             archive(::cereal::make_nvp("MuAlpha", mu_alpha));
             archive(::cereal::make_nvp("MuBeta", mu_beta));
             archive(::cereal::make_nvp("TauAlpha", tau_alpha));
             archive(::cereal::make_nvp("TauBeta", tau_beta));
             archive(::cereal::make_nvp("Scale", scale));
             archive(::cereal::make_nvp("MaxDepth", max_depth));
             archive(::cereal::make_nvp("TauPrimaries", tau_primaries));
+        } else {
             throw std::runtime_error("LeptonDepthFunction only supports version <= 0!");
         }
     }
@@ -83,6 +83,7 @@ friend cereal::access;
 } // namespace siren
 
 CEREAL_CLASS_VERSION(siren::distributions::LeptonDepthFunction, 0);
+CEREAL_REGISTER_TYPE(siren::distributions::LeptonDepthFunction);
 CEREAL_REGISTER_POLYMORPHIC_RELATION(siren::distributions::DepthFunction, siren::distributions::LeptonDepthFunction);
 
 #endif // SIREN_LeptonDepthFunction_H
diff --git a/...ibutions/public/SIREN/distributions/secondary/vertex/SecondaryBoundedVertexDistribution.h b/...ibutions/public/SIREN/distributions/secondary/vertex/SecondaryBoundedVertexDistribution.h
@@ -15,6 +15,7 @@
 #include <cereal/types/polymorphic.hpp>
 #include <cereal/types/base_class.hpp>
 #include <cereal/types/utility.hpp>
+#include <cereal/types/memory.hpp>
 
 #include "SIREN/dataclasses/InteractionTree.h"
 #include "SIREN/distributions/secondary/vertex/SecondaryVertexPositionDistribution.h"
@@ -55,6 +56,7 @@ friend cereal::access;
     void save(Archive & archive, std::uint32_t const version) const {
         if(version == 0) {
             archive(::cereal::make_nvp("MaxLength", max_length));
+            archive(::cereal::make_nvp("FidVol", fiducial_volume));
             archive(cereal::virtual_base_class<SecondaryVertexPositionDistribution>(this));
         } else {
             throw std::runtime_error("SecondaryBoundedVertexDistribution only supports version <= 0!");
@@ -64,8 +66,10 @@ friend cereal::access;
     static void load_and_construct(Archive & archive, cereal::construct<SecondaryBoundedVertexDistribution> & construct, std::uint32_t const version) {
         if(version == 0) {
             double max_length;
+            std::shared_ptr<siren::geometry::Geometry> fiducial_volume;
             archive(::cereal::make_nvp("MaxLength", max_length));
-            construct(max_length);
+            archive(::cereal::make_nvp("FidVol", fiducial_volume));
+            construct(fiducial_volume,max_length);
             archive(cereal::virtual_base_class<SecondaryVertexPositionDistribution>(construct.ptr()));
         } else {
             throw std::runtime_error("SecondaryBoundedVertexDistribution only supports version <= 0!");

diff --git a/...butions/public/SIREN/distributions/secondary/vertex/SecondaryPhysicalVertexDistribution.h b/...butions/public/SIREN/distributions/secondary/vertex/SecondaryPhysicalVertexDistribution.h
@@ -15,6 +15,7 @@
 #include <cereal/types/polymorphic.hpp>
 #include <cereal/types/base_class.hpp>
 #include <cereal/types/utility.hpp>
+#include <cereal/types/memory.hpp>
 
 #include "SIREN/dataclasses/InteractionTree.h"
 #include "SIREN/distributions/secondary/vertex/SecondaryVertexPositionDistribution.h"

diff --git a/...butions/public/SIREN/distributions/secondary/vertex/SecondaryVertexPositionDistribution.h b/...butions/public/SIREN/distributions/secondary/vertex/SecondaryVertexPositionDistribution.h
@@ -13,6 +13,7 @@
 #include <cereal/types/polymorphic.hpp>
 #include <cereal/types/base_class.hpp>
 #include <cereal/types/utility.hpp>
+#include <cereal/types/memory.hpp>
 
 #include "SIREN/dataclasses/InteractionTree.h"  // for InteractionT...
 #include "SIREN/distributions/Distributions.h"  // for WeightableDi...

diff --git a/projects/injection/CMakeLists.txt b/projects/injection/CMakeLists.txt
@@ -4,12 +4,7 @@ LIST (APPEND injection_SOURCES
     ${PROJECT_SOURCE_DIR}/projects/injection/private/Process.cxx
     ${PROJECT_SOURCE_DIR}/projects/injection/private/Injector.cxx
     ${PROJECT_SOURCE_DIR}/projects/injection/private/WeightingUtils.cxx
-    ${PROJECT_SOURCE_DIR}/projects/injection/private/TreeWeighter.cxx
     ${PROJECT_SOURCE_DIR}/projects/injection/private/Weighter.cxx
-    #${PROJECT_SOURCE_DIR}/projects/injection/private/ColumnDepthSIREN.cxx
-    #${PROJECT_SOURCE_DIR}/projects/injection/private/CylinderVolumeSIREN.cxx
-    #${PROJECT_SOURCE_DIR}/projects/injection/private/DecayRangeSIREN.cxx
-    #${PROJECT_SOURCE_DIR}/projects/injection/private/RangedSIREN.cxx
 )
 add_library(SIREN_injection OBJECT ${injection_SOURCES})
 set_property(TARGET SIREN_injection PROPERTY POSITION_INDEPENDENT_CODE ON)
@@ -21,6 +16,7 @@ target_include_directories(SIREN_injection PUBLIC
 target_link_libraries(SIREN_injection
     PRIVATE
         $<BUILD_INTERFACE:rk_static>
+        pybind11::embed
     PUBLIC
         photospline
         SIREN_serialization
@@ -41,10 +37,13 @@ install(DIRECTORY "${PROJECT_SOURCE_DIR}/projects/injection/public/"
 )
 
 #package_add_test(UnitTest_Injector ${PROJECT_SOURCE_DIR}/projects/injection/private/test/Injector_TEST.cxx)
+if(NOT ${CIBUILDWHEEL})
 package_add_test(UnitTest_CCM_HNL ${PROJECT_SOURCE_DIR}/projects/injection/private/test/CCM_HNL_TEST.cxx)
+target_link_libraries(UnitTest_CCM_HNL pybind11::embed)
+endif()
 
 pybind11_add_module(injection ${PROJECT_SOURCE_DIR}/projects/injection/private/pybindings/injection.cxx)
-target_link_libraries(injection PRIVATE SIREN photospline)
+target_link_libraries(injection PRIVATE SIREN photospline pybind11::embed)
 if(DEFINED SKBUILD)
 set_target_properties(injection PROPERTIES
         BUILD_WITH_INSTALL_RPATH FALSE