636 make python serialization usable again (#761)

Author: MaxBetzDLR

cpp/memilio/epidemiology/age_group.h

@@ -34,6 +34,17 @@ struct AgeGroup : public Index<AgeGroup> {
         : Index<AgeGroup>(val)
     {
     }
+
+    /**
+     * Override deserialize of base class
+     * @see mio::Index::deserialize
+     */
+    template <class IOContext>
+    static IOResult<AgeGroup> deserialize(IOContext& io)
+    {
+        BOOST_OUTCOME_TRY(auto&& i, mio::deserialize(io, Tag<size_t>{}));
+        return success(AgeGroup(i));
+    }
 };
 
 } // namespace mio

cpp/memilio/utils/metaprogramming.h

@@ -120,8 +120,8 @@ template <class B1>
 struct disjunction<B1> : B1 {
     //disjunction of one element is identity
 };
-template <class B1, class... Bn>
-struct disjunction<B1, Bn...> : std::conditional<bool(B1::value), B1, disjunction<Bn...>> {
+template<class B1, class... Bn>
+struct disjunction<B1, Bn...> : std::conditional_t<bool(B1::value), B1, disjunction<Bn...>> {
     //disjunction of mutliple elements is equal to the first element if the first element is true.
     //otherwise its equal to the disjunction of the remaining elements.
 };

cpp/models/ode_seir/model.h

@@ -54,6 +54,11 @@ class Model : public FlowModel<InfectionState, Populations<AgeGroup, InfectionSt
     using Base = FlowModel<InfectionState, mio::Populations<AgeGroup, InfectionState>, Parameters, Flows>;
 
 public:
+    Model(const Populations& pop, const ParameterSet& params)
+        : Base(pop, params)
+    {
+    }
+
     Model(int num_agegroups)
         : Base(Populations({AgeGroup(num_agegroups), InfectionState::Count}), ParameterSet(AgeGroup(num_agegroups)))
     {
@@ -201,6 +206,36 @@ class Model : public FlowModel<InfectionState, Populations<AgeGroup, InfectionSt
         auto result = linear_interpolation(t_value, y.get_time(time_late - 1), y.get_time(time_late), y1, y2);
         return mio::success(static_cast<ScalarType>(result));
     }
+
+    /**
+     * serialize this. 
+     * @see mio::serialize
+     */
+    template <class IOContext>
+    void serialize(IOContext& io) const
+    {
+        auto obj = io.create_object("Model");
+        obj.add_element("Parameters", parameters);
+        obj.add_element("Populations", populations);
+    }
+
+    /**
+     * deserialize an object of this class.
+     * @see mio::deserialize
+     */
+    template <class IOContext>
+    static IOResult<Model> deserialize(IOContext& io)
+    {
+        auto obj = io.expect_object("Model");
+        auto par = obj.expect_element("Parameters", Tag<ParameterSet>{});
+        auto pop = obj.expect_element("Populations", Tag<Populations>{});
+        return apply(
+            io,
+            [](auto&& par_, auto&& pop_) {
+                return Model{pop_, par_};
+            },
+            par, pop);
+    }
 };
 
 } // namespace oseir

cpp/models/ode_sir/model.h

@@ -42,6 +42,11 @@ class Model : public CompartmentalModel<InfectionState, Populations<AgeGroup, In
     using Base = CompartmentalModel<InfectionState, mio::Populations<AgeGroup, InfectionState>, Parameters>;
 
 public:
+    Model(const Populations& pop, const ParameterSet& params)
+        : Base(pop, params)
+    {
+    }
+    
     Model(int num_agegroups)
         : Base(Populations({AgeGroup(num_agegroups), InfectionState::Count}), ParameterSet(AgeGroup(num_agegroups)))
     {
@@ -80,6 +85,36 @@ class Model : public CompartmentalModel<InfectionState, Populations<AgeGroup, In
 
         }
     }
+
+    /**
+     * serialize this. 
+     * @see mio::serialize
+     */
+    template <class IOContext>
+    void serialize(IOContext& io) const
+    {
+        auto obj = io.create_object("Model");
+        obj.add_element("Parameters", parameters);
+        obj.add_element("Populations", populations);
+    }
+
+    /**
+     * deserialize an object of this class.
+     * @see mio::deserialize
+     */
+    template <class IOContext>
+    static IOResult<Model> deserialize(IOContext& io)
+    {
+        auto obj = io.expect_object("Model");
+        auto par = obj.expect_element("Parameters", Tag<ParameterSet>{});
+        auto pop = obj.expect_element("Populations", Tag<Populations>{});
+        return apply(
+            io,
+            [](auto&& par_, auto&& pop_) {
+                return Model{pop_, par_};
+            },
+            par, pop);
+    }
 };
 
 } // namespace osir

pycode/memilio-simulation/memilio/simulation/abm.cpp

@@ -33,7 +33,7 @@ namespace py = pybind11;
 
 PYBIND11_MODULE(_simulation_abm, m)
 {
-    pymio::iterable_enum<mio::abm::InfectionState>(m, "InfectionState", py::module_local{})
+    pymio::iterable_enum<mio::abm::InfectionState>(m, "InfectionState")
         .value("Susceptible", mio::abm::InfectionState::Susceptible)
         .value("Exposed", mio::abm::InfectionState::Exposed)
         .value("InfectedNoSymptoms", mio::abm::InfectionState::InfectedNoSymptoms)
@@ -62,21 +62,21 @@ PYBIND11_MODULE(_simulation_abm, m)
         .value("PublicTransport", mio::abm::LocationType::PublicTransport)
         .value("TransportWithoutContact", mio::abm::LocationType::TransportWithoutContact);
 
-    py::class_<mio::abm::TestParameters>(m, "TestParameters")
+    pymio::bind_class<mio::abm::TestParameters, pymio::EnablePickling::Never>(m, "TestParameters")
         .def(py::init<double, double>())
         .def_readwrite("sensitivity", &mio::abm::TestParameters::sensitivity)
         .def_readwrite("specificity", &mio::abm::TestParameters::specificity);
 
     pymio::bind_CustomIndexArray<mio::UncertainValue, mio::abm::VirusVariant, mio::AgeGroup>(m, "_AgeParameterArray");
     pymio::bind_Index<mio::abm::ExposureType>(m, "ExposureTypeIndex");
-    pymio::bind_ParameterSet<mio::abm::ParametersBase>(m, "ParametersBase");
-    py::class_<mio::abm::Parameters, mio::abm::ParametersBase>(m, "Parameters")
+    pymio::bind_ParameterSet<mio::abm::ParametersBase, pymio::EnablePickling::Never>(m, "ParametersBase");
+    pymio::bind_class<mio::abm::Parameters, pymio::EnablePickling::Never, mio::abm::ParametersBase>(m, "Parameters")
         .def(py::init<int>())
         .def("check_constraints", &mio::abm::Parameters::check_constraints);
 
-    pymio::bind_ParameterSet<mio::abm::LocalInfectionParameters>(m, "LocalInfectionParameters").def(py::init<size_t>());
+    pymio::bind_ParameterSet<mio::abm::LocalInfectionParameters, pymio::EnablePickling::Never>(m, "LocalInfectionParameters").def(py::init<size_t>());
 
-    py::class_<mio::abm::TimeSpan>(m, "TimeSpan")
+    pymio::bind_class<mio::abm::TimeSpan, pymio::EnablePickling::Never>(m, "TimeSpan")
         .def(py::init<int>(), py::arg("seconds") = 0)
         .def_property_readonly("seconds", &mio::abm::TimeSpan::seconds)
         .def_property_readonly("hours", &mio::abm::TimeSpan::hours)
@@ -101,7 +101,7 @@ PYBIND11_MODULE(_simulation_abm, m)
     m.def("hours", &mio::abm::hours);
     m.def("days", py::overload_cast<int>(&mio::abm::days));
 
-    py::class_<mio::abm::TimePoint>(m, "TimePoint")
+    pymio::bind_class<mio::abm::TimePoint, pymio::EnablePickling::Never>(m, "TimePoint")
         .def(py::init<int>(), py::arg("seconds") = 0)
         .def_property_readonly("seconds", &mio::abm::TimePoint::seconds)
         .def_property_readonly("days", &mio::abm::TimePoint::days)
@@ -121,7 +121,7 @@ PYBIND11_MODULE(_simulation_abm, m)
         .def(py::self - mio::abm::TimeSpan{})
         .def(py::self -= mio::abm::TimeSpan{});
 
-    py::class_<mio::abm::LocationId>(m, "LocationId")
+    pymio::bind_class<mio::abm::LocationId, pymio::EnablePickling::Never>(m, "LocationId")
         .def(py::init([](uint32_t idx, mio::abm::LocationType type) {
             return mio::abm::LocationId{idx, type};
         }))
@@ -130,36 +130,36 @@ PYBIND11_MODULE(_simulation_abm, m)
         .def(py::self == py::self)
         .def(py::self != py::self);
 
-    py::class_<mio::abm::Person>(m, "Person")
+    pymio::bind_class<mio::abm::Person, pymio::EnablePickling::Never>(m, "Person")
         .def("set_assigned_location", py::overload_cast<mio::abm::LocationId>(&mio::abm::Person::set_assigned_location))
         .def_property_readonly("location", py::overload_cast<>(&mio::abm::Person::get_location, py::const_))
         .def_property_readonly("age", &mio::abm::Person::get_age)
         .def_property_readonly("is_in_quarantine", &mio::abm::Person::is_in_quarantine);
 
-    py::class_<mio::abm::TestingCriteria>(m, "TestingCriteria")
+    pymio::bind_class<mio::abm::TestingCriteria, pymio::EnablePickling::Never>(m, "TestingCriteria")
         .def(py::init<const std::vector<mio::AgeGroup>&, const std::vector<mio::abm::InfectionState>&>(),
              py::arg("age_groups"), py::arg("infection_states"));
+             
+    pymio::bind_class<mio::abm::GenericTest, pymio::EnablePickling::Never>(m, "GenericTest").def(py::init<>());
+    pymio::bind_class<mio::abm::AntigenTest, pymio::EnablePickling::Never, mio::abm::GenericTest>(m, "AntigenTest").def(py::init<>());
+    pymio::bind_class<mio::abm::PCRTest, pymio::EnablePickling::Never, mio::abm::GenericTest>(m, "PCRTest").def(py::init<>());
 
-    py::class_<mio::abm::GenericTest>(m, "GenericTest").def(py::init<>());
-    py::class_<mio::abm::AntigenTest, mio::abm::GenericTest>(m, "AntigenTest").def(py::init<>());
-    py::class_<mio::abm::PCRTest, mio::abm::GenericTest>(m, "PCRTest").def(py::init<>());
-
-    py::class_<mio::abm::TestingScheme>(m, "TestingScheme")
+    pymio::bind_class<mio::abm::TestingScheme, pymio::EnablePickling::Never>(m, "TestingScheme")
         .def(py::init<const mio::abm::TestingCriteria&, mio::abm::TimeSpan, mio::abm::TimePoint, mio::abm::TimePoint,
                       const mio::abm::GenericTest&, double>(),
              py::arg("testing_criteria"), py::arg("testing_min_time_since_last_test"), py::arg("start_date"),
              py::arg("end_date"), py::arg("test_type"), py::arg("probability"))
         .def_property_readonly("active", &mio::abm::TestingScheme::is_active);
 
-    py::class_<mio::abm::Vaccination>(m, "Vaccination")
+    pymio::bind_class<mio::abm::Vaccination, pymio::EnablePickling::Never>(m, "Vaccination")
         .def(py::init<mio::abm::ExposureType, mio::abm::TimePoint>(), py::arg("exposure_type"), py::arg("time"))
         .def_readwrite("exposure_type", &mio::abm::Vaccination::exposure_type)
         .def_readwrite("time", &mio::abm::Vaccination::time);
 
-    py::class_<mio::abm::TestingStrategy>(m, "TestingStrategy")
+    pymio::bind_class<mio::abm::TestingStrategy, pymio::EnablePickling::Never>(m, "TestingStrategy")
         .def(py::init<const std::unordered_map<mio::abm::LocationId, std::vector<mio::abm::TestingScheme>>&>());
 
-    py::class_<mio::abm::Location>(m, "Location")
+    pymio::bind_class<mio::abm::Location, pymio::EnablePickling::Never>(m, "Location")
         .def_property_readonly("type", &mio::abm::Location::get_type)
         .def_property_readonly("index", &mio::abm::Location::get_index)
         .def_property("infection_parameters",
@@ -172,7 +172,7 @@ PYBIND11_MODULE(_simulation_abm, m)
     pymio::bind_Range<decltype(std::declval<mio::abm::World>().get_locations())>(m, "_WorldLocationsRange");
     pymio::bind_Range<decltype(std::declval<mio::abm::World>().get_persons())>(m, "_WorldPersonsRange");
 
-    py::class_<mio::abm::Trip>(m, "Trip")
+    pymio::bind_class<mio::abm::Trip, pymio::EnablePickling::Never>(m, "Trip")
         .def(py::init<uint32_t, mio::abm::TimePoint, mio::abm::LocationId, mio::abm::LocationId,
                       std::vector<uint32_t>>(),
              py::arg("person_id"), py::arg("time"), py::arg("destination"), py::arg("origin"),
@@ -183,13 +183,13 @@ PYBIND11_MODULE(_simulation_abm, m)
         .def_readwrite("origin", &mio::abm::Trip::migration_origin)
         .def_readwrite("cells", &mio::abm::Trip::cells);
 
-    py::class_<mio::abm::TripList>(m, "TripList")
+    pymio::bind_class<mio::abm::TripList, pymio::EnablePickling::Never>(m, "TripList")
         .def(py::init<>())
         .def("add_trip", &mio::abm::TripList::add_trip, py::arg("trip"), py::arg("weekend") = false)
         .def("next_trip", &mio::abm::TripList::get_next_trip, py::arg("weekend") = false)
         .def("num_trips", &mio::abm::TripList::num_trips, py::arg("weekend") = false);
 
-    py::class_<mio::abm::World>(m, "World")
+    pymio::bind_class<mio::abm::World, pymio::EnablePickling::Never>(m, "World")
         .def(py::init<int32_t>())
         .def("add_location", &mio::abm::World::add_location, py::arg("location_type"), py::arg("num_cells") = 1)
         .def("add_person", &mio::abm::World::add_person, py::arg("location_id"), py::arg("age_group"),
@@ -213,7 +213,7 @@ PYBIND11_MODULE(_simulation_abm, m)
             },
             py::return_value_policy::reference_internal);
 
-    py::class_<mio::abm::Simulation>(m, "Simulation")
+    pymio::bind_class<mio::abm::Simulation, pymio::EnablePickling::Never>(m, "Simulation")
         .def(py::init<mio::abm::TimePoint, size_t>())
         .def("advance",
              static_cast<void (mio::abm::Simulation::*)(mio::abm::TimePoint)>(&mio::abm::Simulation::advance),

pycode/memilio-simulation/memilio/simulation/compartments/compartmentalmodel.h

@@ -21,6 +21,7 @@
 #define PYMIO_COMPARTMENTALMODEL_H
 
 #include "memilio/compartments/compartmentalmodel.h"
+#include "pybind_util.h"
 
 #include "pybind11/pybind11.h"
 
@@ -30,22 +31,28 @@ namespace pymio
 /*
  * @brief bind a compartmental model for any Populations and Parameters class
  */
-template <class InfectionState, class Populations, class Parameters>
+template <class InfectionState, class Populations, class Parameters, EnablePickling F>
 void bind_CompartmentalModel(pybind11::module_& m, std::string const& name)
 {
     using Model = mio::CompartmentalModel<InfectionState, Populations, Parameters>;
-    pybind11::class_<Model>(m, name.c_str())
+    bind_class<Model, F>(m, name.c_str())
         .def(pybind11::init<Populations const&, Parameters const&>())
         .def("apply_constraints", &Model::template apply_constraints)
         .def("check_constraints", &Model::template check_constraints)
         .def("get_initial_values", &Model::get_initial_values)
         .def_property(
-            "populations", [](const Model& self) -> auto& { return self.populations; },
+            "populations",
+            [](const Model& self) -> auto& {
+                return self.populations;
+            },
             [](Model& self, Populations& p) {
                 self.populations = p;
             })
         .def_property(
-            "parameters", [](const Model& self) -> auto& { return self.parameters; },
+            "parameters",
+            [](const Model& self) -> auto& {
+                return self.parameters;
+            },
             [](Model& self, Parameters& p) {
                 self.parameters = p;
             });

pycode/memilio-simulation/memilio/simulation/compartments/flow_simulation.h

@@ -21,16 +21,17 @@
 #define PYMIO_FLOW_SIMULATION_H
 
 #include "memilio/compartments/flow_simulation.h"
+#include "pybind_util.h"
 
 #include "pybind11/pybind11.h"
 
 namespace pymio
 {
 
-template <class Model>
+template <class Model, EnablePickling F>
 void bind_Flow_Simulation(pybind11::module_& m)
 {
-    pybind11::class_<mio::FlowSimulation<Model>>(m, "FlowSimulation")
+    bind_class<mio::FlowSimulation<Model>, F>(m, "FlowSimulation")
         .def(pybind11::init<const Model&, double, double>(), pybind11::arg("model"), pybind11::arg("t0") = 0,
              pybind11::arg("dt") = 0.1)
         .def_property_readonly("result",

pycode/memilio-simulation/memilio/simulation/compartments/simulation.h

@@ -21,6 +21,7 @@
 #define PYMIO_SIMULATION_H
 
 #include "memilio/compartments/simulation.h"
+#include "pybind_util.h"
 
 #include "pybind11/pybind11.h"
 
@@ -33,7 +34,7 @@ namespace pymio
 template <class Simulation>
 void bind_Simulation(pybind11::module_& m, std::string const& name)
 {
-    pybind11::class_<Simulation>(m, name.c_str())
+    bind_class<Simulation, EnablePickling::IfAvailable>(m, name.c_str())
         .def(pybind11::init<const typename Simulation::Model&, double, double>(), pybind11::arg("model"),
              pybind11::arg("t0") = 0, pybind11::arg("dt") = 0.1)
         .def_property_readonly("result", pybind11::overload_cast<>(&Simulation::get_result, pybind11::const_),

pycode/memilio-simulation/memilio/simulation/epidemiology/damping_sampling.cpp

@@ -32,7 +32,7 @@ namespace pymio
 
 void bind_damping_sampling(py::module_& m, std::string const& name)
 {
-    pymio::pybind_pickle_class<mio::DampingSampling>(m, name.c_str())
+    bind_class<mio::DampingSampling, EnablePickling::Required>(m, name.c_str())
         .def(py::init([](const mio::UncertainValue& value, int level, int type, double time,
                          const std::vector<size_t>& matrices, const Eigen::Ref<const Eigen::VectorXd>& groups) {
                  return mio::DampingSampling(value, mio::DampingLevel(level), mio::DampingType(type),

pycode/memilio-simulation/memilio/simulation/epidemiology/dynamic_npis.h

@@ -36,7 +36,7 @@ void bind_dynamicNPI_members(pybind11::module_& m, std::string const& name)
 {
     bind_Range<decltype(std::declval<mio::DynamicNPIs>().get_thresholds())>(m, "_ThresholdRange");
     using C = mio::DynamicNPIs;
-    pybind11::class_<C>(m, name.c_str())
+    bind_class<C, EnablePickling::Required>(m, name.c_str())
         .def(pybind11::init<>())
         .def_property(
             "interval",