Start to replace old back-end with the new

molpopgen · Nov 25, 2020 · 15a8cff · 15a8cff
1 parent 80f15c8
commit 15a8cff
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Showing 11 changed files with 24 additions and 107 deletions.
diff --git a/fwdpy11/CMakeLists.txt b/fwdpy11/CMakeLists.txt
@@ -11,13 +11,7 @@ set(FWDPP_TYPES_SOURCES src/fwdpp_types/init.cc ;
     src/fwdpp_types/EdgeTable.cc
     src/fwdpp_types/MutationTable.cc
     src/fwdpp_types/SiteTable.cc
-    src/fwdpp_types/TableCollection.cc
-    src/fwdpp_types/GeneticMapUnit.cc 
-    src/fwdpp_types/PoissonInterval.cc 
-    src/fwdpp_types/BinomialPoint.cc
-    src/fwdpp_types/PoissonPoint.cc
-    src/fwdpp_types/FixedCrossovers.cc
-    src/fwdpp_types/BinomialInterval.cc)
+    src/fwdpp_types/TableCollection.cc)
 
 
 set(FWDPY11_TYPES_SOURCES src/fwdpy11_types/init.cc
@@ -32,7 +26,8 @@ set(FWDPY11_TYPES_SOURCES src/fwdpy11_types/init.cc
     src/fwdpy11_types/DiploidPopulation.cc
     src/fwdpy11_types/ts_from_tskit.cc
     src/fwdpy11_types/tsrecorders.cc
-    src/fwdpy11_types/RecordNothing.cc)
+    src/fwdpy11_types/RecordNothing.cc
+    src/fwdpy11_types/GeneticMapUnit.cc)
 
 set(REGION_SOURCES src/regions/init.cc src/regions/Region.cc src/regions/Sregion.cc src/regions/GammaS.cc src/regions/ConstantS.cc
     src/regions/ExpS.cc src/regions/UniformS.cc src/regions/GaussianS.cc src/regions/MutationRegions.cc

diff --git a/fwdpy11/genetic_map_unit.py b/fwdpy11/genetic_map_unit.py
@@ -66,9 +66,12 @@ class PoissonInterval(fwdpy11._fwdpy11._ll_PoissonInterval):
     beg: float
     end: float
     mean: float
+    discrete: bool = True
 
     def __attrs_post_init__(self):
-        super(PoissonInterval, self).__init__(self.beg, self.end, self.mean)
+        super(PoissonInterval, self).__init__(
+            self.beg, self.end, self.mean, self.discrete
+        )
 
 
 @attr_add_asblack

diff --git a/fwdpy11/src/fwdpp_types/BinomialInterval.cc b/fwdpy11/src/fwdpp_types/BinomialInterval.cc
diff --git a/fwdpy11/src/fwdpp_types/BinomialPoint.cc b/fwdpy11/src/fwdpp_types/BinomialPoint.cc
diff --git a/fwdpy11/src/fwdpp_types/FixedCrossovers.cc b/fwdpy11/src/fwdpp_types/FixedCrossovers.cc
diff --git a/fwdpy11/src/fwdpp_types/GeneticMapUnit.cc b/fwdpy11/src/fwdpp_types/GeneticMapUnit.cc
diff --git a/fwdpy11/src/fwdpp_types/PoissonInterval.cc b/fwdpy11/src/fwdpp_types/PoissonInterval.cc
diff --git a/fwdpy11/src/fwdpp_types/PoissonPoint.cc b/fwdpy11/src/fwdpp_types/PoissonPoint.cc
diff --git a/fwdpy11/src/fwdpp_types/init.cc b/fwdpy11/src/fwdpp_types/init.cc
@@ -18,12 +18,6 @@ void init_ts_EdgeTable(py::module &m);
 void init_ts_MutationTable(py::module &);
 void init_ts_SiteTable(py::module &);
 void init_ts_TableCollection(py::module &);
-void init_GeneticMapUnit(py::module &);
-void init_PoissonInterval(py::module &);
-void init_BinomialPoint(py::module &);
-void init_PoissonPoint(py::module &);
-void init_FixedCrossovers(py::module &);
-void init_BinomialInterval(py::module &);
 
 void
 initialize_fwdpp_types(py::module &m)
@@ -43,13 +37,6 @@ initialize_fwdpp_types(py::module &m)
     init_HaploidGenome(m);
     init_data_matrix(m);
 
-    init_GeneticMapUnit(m);
-    init_PoissonInterval(m);
-    init_BinomialPoint(m);
-    init_PoissonPoint(m);
-    init_FixedCrossovers(m);
-    init_BinomialInterval(m);
-
     // Types related to tree sequenc recording
     init_NULL_NODE(m);
     init_ts_Node(m);

diff --git a/fwdpy11/src/fwdpy11_types/GeneticMapUnit.cc b/fwdpy11/src/fwdpy11_types/GeneticMapUnit.cc
@@ -0,0 +1,15 @@
+#include <pybind11/pybind11.h>
+#include <fwdpy11/regions/GeneticMapUnit.hpp>
+
+namespace py = pybind11;
+
+void
+init_GeneticMapUnit(py::module& m)
+{
+    py::class_<fwdpy11::GeneticMapUnit>(m, "_ll_GeneticMapUnit");
+
+    py::class_<fwdpy11::PoissonInterval, fwdpy11::GeneticMapUnit>(m,
+                                                                  "_ll_PoissonInterval")
+        .def(py::init<double, double, double, bool>(), py::kw_only(), py::arg("begin"),
+             py::arg("end"), py::arg("mean"), py::arg("discrete") = true);
+}
diff --git a/fwdpy11/src/fwdpy11_types/init.cc b/fwdpy11/src/fwdpy11_types/init.cc
@@ -14,6 +14,7 @@ void init_DiploidPopulation(py::module & m);
 void init_tsrecorders(py::module & m);
 void
 init_RecordNothing(pybind11::module &);
+void init_GeneticMapUnit(pybind11::module &);
 
 void initialize_fwdpy11_types(py::module & m)
 {
@@ -28,4 +29,5 @@ void initialize_fwdpy11_types(py::module & m)
     init_DiploidPopulation(m);
     init_RecordNothing(m);
     init_tsrecorders(m);
+    init_GeneticMapUnit(m);
 }