[bind] bind specified in #48

src/database.cpp

@@ -1,4 +1,5 @@
 #include "database.hpp"
+#include "config.hpp"
 
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
@@ -160,17 +161,163 @@ static py::dict get_hist_transition_matrix(DataBase<int> &self,
   return ret;
 }
 
+static py::dict get_hist_virus(DataBase<int> &self) {
+  std::vector<std::string> *states = new std::vector<std::string>();
+  std::vector<int> *dates = new std::vector<int>();
+  std::vector<int> *ids = new std::vector<int>();
+  std::vector<int> *counts = new std::vector<int>();
+
+  self.get_hist_virus(*dates, *ids, *states, *counts);
+
+  /* Return to Python. */
+  py::capsule pyc_dates(
+      dates, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+  py::capsule pyc_ids(
+      ids, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+  py::capsule pyc_counts(
+      counts, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+
+  py::array py_dates(dates->size(), dates->data(), pyc_dates);
+  py::array py_ids(ids->size(), ids->data(), pyc_ids);
+  py::array py_counts(counts->size(), counts->data(), pyc_counts);
+
+  py::dict ret("dates"_a = dates, "ids"_a = py_ids, "states"_a = states,
+               "counts"_a = py_counts);
+
+  return ret;
+}
+
+static py::dict get_hist_tool(DataBase<int> &self) {
+  std::vector<std::string> *states = new std::vector<std::string>();
+  std::vector<int> *dates = new std::vector<int>();
+  std::vector<int> *ids = new std::vector<int>();
+  std::vector<int> *counts = new std::vector<int>();
+
+  self.get_hist_tool(*dates, *ids, *states, *counts);
+
+  /* Return to Python. */
+  py::capsule pyc_dates(
+      dates, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+  py::capsule pyc_ids(
+      ids, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+  py::capsule pyc_counts(
+      counts, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+
+  py::array py_dates(dates->size(), dates->data(), pyc_dates);
+  py::array py_ids(ids->size(), ids->data(), pyc_ids);
+  py::array py_counts(counts->size(), counts->data(), pyc_counts);
+
+  py::dict ret("dates"_a = dates, "ids"_a = py_ids, "states"_a = states,
+               "counts"_a = py_counts);
+
+  return ret;
+}
+
+static py::dict get_today_transition_matrix(DataBase<int> &self) {
+  std::vector<int> *counts = new std::vector<int>();
+
+  self.get_today_transition_matrix(*counts);
+
+  /* Return to Python. */
+  py::capsule pyc_counts(
+      counts, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+
+  py::array py_counts(counts->size(), counts->data(), pyc_counts);
+
+  py::dict ret("counts"_a = py_counts);
+
+  return ret;
+}
+
+static py::dict get_today_virus(DataBase<int> &self) {
+  std::vector<std::string> *states = new std::vector<std::string>();
+  std::vector<int> *ids = new std::vector<int>();
+  std::vector<int> *counts = new std::vector<int>();
+
+  self.get_today_virus(*states, *ids, *counts);
+
+  /* Return to Python. */
+  py::capsule pyc_ids(
+      ids, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+  py::capsule pyc_counts(
+      counts, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+
+  py::array py_ids(ids->size(), ids->data(), pyc_ids);
+  py::array py_counts(counts->size(), counts->data(), pyc_counts);
+
+  py::dict ret("states"_a = states, "ids"_a = py_ids, "counts"_a = py_counts);
+
+  return ret;
+}
+
+static py::dict get_today_total(DataBase<int> &self) {
+  std::vector<std::string> *states = new std::vector<std::string>();
+  std::vector<int> *counts = new std::vector<int>();
+
+  self.get_today_total(states, counts);
+
+  /* Return to Python. */
+  py::capsule pyc_counts(
+      counts, [](void *x) { delete reinterpret_cast<std::vector<int> *>(x); });
+
+  py::array py_counts(counts->size(), counts->data(), pyc_counts);
+
+  py::dict ret("states"_a = states, "counts"_a = py_counts);
+
+  return ret;
+}
+
 void epiworldpy::export_database(
     py::class_<epiworld::DataBase<int>,
                std::shared_ptr<epiworld::DataBase<int>>> &c) {
-  c.def("get_hist_total", &get_hist_total,
-        "Get historical totals for this model run.")
+  c.def("add_user_data",
+        pybind11::detail::overload_cast_impl<std::vector<epiworld_double>>()(
+            &epiworld::DataBase<int>::add_user_data),
+        "Add a list of user data.")
+      .def("add_user_data",
+           pybind11::detail::overload_cast_impl<epiworld_fast_uint,
+                                                epiworld_double>()(
+               &epiworld::DataBase<int>::add_user_data),
+           "Add a list of user data.")
+      .def("get_n_tools", &epiworld::DataBase<int>::get_n_tools,
+           "Get the number of tools.")
+      .def("get_n_viruses", &epiworld::DataBase<int>::get_n_viruses,
+           "Get the number of viruses.")
+      .def("record_transmission", &epiworld::DataBase<int>::record_transmission,
+           "Record a transmission event.")
+      .def("write_data", &epiworld::DataBase<int>::write_data,
+           "Write some data.")
+      .def("get_hist_virus", &get_hist_virus, "Get historical virus data.")
+      .def("get_hist_tool", &get_hist_tool, "Get historical tool data.")
+      .def("get_today_transition_matrix", &get_today_transition_matrix,
+           "Get today's transition matrix.")
+      .def("get_today_virus", &get_today_virus, "Get today's virus data.")
+      //.def("get_today_total", pybind11::detail::overload_cast_impl<epiworld_fast_uint>()(&epiworld::DataBase<int>::get_today_total), "Get today's total data.")
+      .def("get_today_total", &get_today_total, "Get today's total data.")
+      .def("size", &epiworld::DataBase<int>::size,
+           "Get the size (number of entries).")
+      .def("record", &epiworld::DataBase<int>::record,
+           "Register a new variant.")                                       // ?
+      .def("reset", &epiworld::DataBase<int>::reset, "Reset the database.") // ?
+      /* FIXME: This should work, as PyBind should automatically convert the
+       * lambda into a py::cpp_function, but I should double check this. */
+      .def("set_seq_hasher", &epiworld::DataBase<int>::set_seq_hasher,
+           "Set the sequence hashing function.")
+      .def("record_tool", &epiworld::DataBase<int>::record_tool,
+           "Add a new tool to the database.")
+      .def("record_virus", &epiworld::DataBase<int>::record_virus,
+           "Add a new virus to the database.")
+      .def("get_hist_total", &get_hist_total,
+           "Get historical totals for this model run.")
       .def("get_reproductive_number", &get_reproductive_number,
            "Get reproductive numbers over time for every virus in the model.")
       .def("get_transmissions", &get_transmissions,
            "Get transmission data over time for every virus in the model.")
       .def("get_generation_time", &get_generation_time,
            "Get generation times over time for every virus in the model.")
       .def("get_hist_transition_matrix", &get_hist_transition_matrix,
-           "Get historical transitions in a tabular format.");
+           "Get historical transitions in a tabular format.")
+      .def("get_transition_probability",
+           &epiworld::DataBase<int>::transition_probability,
+           "Get the transition probably.");
 }