Fix tests

Author: MaxBetzDLR

cpp/models/ode_secir/parameters_io.cpp

@@ -306,7 +306,7 @@ IOResult<void> set_population_data(Model<ScalarType>& model, const std::vector<S
                                                                              total);
     }
 
-    for (auto i = AgeGroup(0); i < AgeGroup(6); i++) {
+    for (auto i = AgeGroup(0); i < num_groups; i++) {
         for (auto j = Index<InfectionState>(0); j < InfectionState::Count; ++j) {
             if (model.populations[{i, j}] < 0) {
                 log_warning("Compartment at age group {}, infection state {}, is negative: {}", size_t(i), size_t(j),

cpp/tests/test_odesecir.cpp

@@ -1551,7 +1551,6 @@ TEST(TestOdeSecirIO, read_input_data_county_aggregates_one_group)
     models1[0].property.parameters.get<mio::osecir::CriticalPerSevere<double>>()[mio::AgeGroup(0)]         = 0.25;
 
     auto pydata_dir_Germany = mio::path_join(TEST_DATA_DIR, "Germany", "pydata");
-    const std::vector<int> counties{1002};
     const auto date = mio::Date(2020, 12, 1);
 
     std::vector<double> scale6(num_age_groups, 1.0);

pycode/memilio-simulation/memilio/simulation/bindings/models/osecir.cpp

@@ -305,7 +305,7 @@ PYBIND11_MODULE(_simulation_osecir, m)
             auto node_ids = pymio::check_and_throw(mio::get_node_ids(mio::path_join(pydata_path, "county_current_population.json"), true));
 
             mio::Graph<mio::osecir::Model<double>, mio::MobilityParameters<double>> params_graph(node_ids, 
-            mio::osecir::Model<double>::Populations({params.get_num_groups(), mio::osecir::InfectionState::Count}), params);
+                mio::osecir::Model<double>::Populations({params.get_num_groups(), mio::osecir::InfectionState::Count}), params);
             pymio::check_and_throw(mio::osecir::read_input_data(params_graph.nodes(), start_date, scaling_factor_inf, scaling_factor_icu, 
                             mio::regions::de::EpidataFilenames::county(pydata_path)));
 

pycode/memilio-simulation/memilio/simulation/bindings/models/osecirvvs.cpp

@@ -336,29 +336,30 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
     pymio::bind_read_graph<mio::osecirvvs::Model<double>>(m);
     m.def(
         "read_input_data_german_county",
-        [](mio::Graph<mio::osecirvvs::Model<double>, mio::MobilityParameters<double>>& params_graph, mio::Date start_date,
-           const std::vector<double>& scaling_factor_inf, double scaling_factor_icu, std::string& pydata_path) {
+        [](mio::Graph<mio::osecirvvs::Model<double>, mio::MobilityParameters<double>>& params_graph, 
+           mio::Date start_date, const std::vector<double>& scaling_factor_inf, double scaling_factor_icu, 
+           int num_days, std::string& pydata_path) {
 
             auto result = mio::osecirvvs::read_input_data(params_graph.nodes(), start_date, scaling_factor_inf, scaling_factor_icu, 
-                            mio::regions::de::EpidataFilenames::county(pydata_path));
+                            num_days, mio::regions::de::EpidataFilenames::county(pydata_path));
             return pymio::check_and_throw(result);
         },
         "Reads compartments for german counties at a specified date from data files.",
         py::arg("params_graph"), py::arg("start_date"), py::arg("scaling_factor_inf"), py::arg("scaling_factor_icu"),
-        py::arg("pydata_path"), py::return_value_policy::move);
+        py::arg("num_days"), py::arg("pydata_path"), py::return_value_policy::move);
 
     m.def(
         "create_graph_german_county",
         [](const mio::osecirvvs::Parameters<double>& params, mio::Date start_date, mio::Date end_date,
-           const std::vector<double>& scaling_factor_inf, double scaling_factor_icu, std::string& pydata_path,
-           double tnt_capacity_factor) {
+           const std::vector<double>& scaling_factor_inf, double scaling_factor_icu, int num_days, 
+           std::string& pydata_path, double tnt_capacity_factor) {
 
             auto node_ids = pymio::check_and_throw(mio::get_node_ids(mio::path_join(pydata_path, "county_current_population.json"), true));
 
             mio::Graph<mio::osecirvvs::Model<double>, mio::MobilityParameters<double>> params_graph(node_ids, 
-            mio::osecirvvs::Model<double>::Populations({params.get_num_groups(), mio::osecirvvs::InfectionState::Count}), params);
-            pymio::check_and_throw(mio::osecirvvs::read_input_data(params_graph.nodes(), start_date, scaling_factor_inf, scaling_factor_icu, 
-                            mio::regions::de::EpidataFilenames::county(pydata_path)));
+                mio::osecirvvs::Model<double>::Populations({params.get_num_groups(), mio::osecirvvs::InfectionState::Count}), params);
+            pymio::check_and_throw(mio::osecirvvs::read_input_data(params_graph.nodes(), start_date, 
+                            scaling_factor_inf, scaling_factor_icu, num_days, mio::regions::de::EpidataFilenames::county(pydata_path)));
 
             mio::set_test_and_trace_capacity<mio::osecirvvs::Model<double>, mio::osecirvvs::TestAndTraceCapacity<double>>(params_graph.nodes(), tnt_capacity_factor);
             mio::set_german_holidays<double, mio::osecirvvs::Model<double>, mio::osecirvvs::ContactPatterns<double>>(params_graph.nodes(), start_date, end_date);
@@ -368,7 +369,7 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
         },
         "Creates graph of germany with compartments for geographic units at a specified date from data files.",
         py::arg("params"), py::arg("start_date"), py::arg("end_date"), py::arg("scaling_factor_inf"), 
-        py::arg("scaling_factor_icu"), py::arg("pydata_path"), py::arg("tnt_capacity_factor"),
+        py::arg("scaling_factor_icu"), py::arg("num_days"), py::arg("pydata_path"), py::arg("tnt_capacity_factor"),
         py::return_value_policy::move);
 #endif // MEMILIO_HAS_JSONCPP