#308 Replace deprecated functions

ecell4/core/Context.hpp

@@ -469,6 +469,12 @@ class rule_based_expression_matcher<std::vector<Species> >
  * New interfaces for the rule-based modeling
  */
 
+inline Integer count_species_matches(const Species& pttrn, const Species& sp)
+{
+    return static_cast<Integer>(
+        context::rule_based_expression_matcher<Species>(pttrn).count(sp));
+}
+
 inline Species format_species(const Species& sp)
 {
     return context::format_species(sp);

ecell4/core/Species.cpp

@@ -29,7 +29,7 @@ bool Species::operator>(const Species& rhs) const
 Integer Species::count(const Species& sp) const
 {
     // return count_spmatches(*this, sp);
-    throw NotSupported("deprecated");
+    throw NotSupported("Function 'Species::count' is deprecated. Rather use 'count_species_matches'");
 }
 
 void Species::add_unit(const UnitSpecies& usp)

python/lib/ecell4/Species.pxi

@@ -334,30 +334,26 @@ cdef Species Species_from_Cpp_Species(Cpp_Species *sp):
 # 
 #     """
 #     return context.spmatch(deref(pttrn.thisptr), deref(sp.thisptr))
-# 
-# def count_spmatches(Species pttrn, Species sp):
-#     """count_spmatches(pttrn, sp) -> Integer
-# 
-#     Count the number of matches for a pattern given as a ``Species``.
-# 
-#     Parameters
-#     ----------
-#     pttrn : Species
-#         A pattern.
-#     sp : Species
-#         A target.
-# 
-#     Returns
-#     -------
-#     Integer:
-#         The number of matches.
-# 
-#     Notes
-#     -----
-#     Rather use ``Species.count``.
-# 
-#     """
-#     return context.count_spmatches(deref(pttrn.thisptr), deref(sp.thisptr))
+
+def count_species_matches(Species pttrn, Species sp):
+    """count_species_matches(pttrn, sp) -> Integer
+
+    Count the number of matches for a pattern given as a ``Species``.
+
+    Parameters
+    ----------
+    pttrn : Species
+        A pattern.
+    sp : Species
+        A target.
+
+    Returns
+    -------
+    Integer:
+        The number of matches.
+
+    """
+    return context.count_species_matches(deref(pttrn.thisptr), deref(sp.thisptr))
 
 def format_species(Species sp):
     """format_species(sp) -> Species

python/lib/ecell4/context.pxd

@@ -12,6 +12,7 @@ from core cimport Cpp_Species, Cpp_ReactionRule
 
 cdef extern from "ecell4/core/Context.hpp" namespace "ecell4":
     Cpp_Species format_species(Cpp_Species&)
+    Integer count_species_matches(Cpp_Species, Cpp_Species)
     # string unique_serial(Cpp_Species&)
 
     # bool spmatch(Cpp_Species, Cpp_Species)

python/tests/core/test_context.py

@@ -10,17 +10,17 @@ def setUp(self):
 
     def test1(self):
         sp1 = Species("A")
-        self.assertEqual(sp1.count(Species("A")), 1)
-        self.assertEqual(sp1.count(Species("A.A")), 2)
+        self.assertEqual(count_species_matches(sp1, Species("A")), 1)
+        self.assertEqual(count_species_matches(sp1, Species("A.A")), 2)
 
     def test2(self):
         sp1 = Species("A.B")
-        self.assertEqual(sp1.count(Species("A.B")), 1)
-        self.assertEqual(sp1.count(Species("B.A")), 1)
+        self.assertEqual(count_species_matches(sp1, Species("A.B")), 1)
+        self.assertEqual(count_species_matches(sp1, Species("B.A")), 1)
 
     def test3(self):
         sp1 = Species("A(p=u^_)")
-        self.assertEqual(sp1.count(Species("A(p=u^1).B(b^1)")), 1)
+        self.assertEqual(count_species_matches(sp1, Species("A(p=u^1).B(b^1)")), 1)
 
 
 if __name__ == "__main__":

python/tests/core/test_species.py

@@ -18,7 +18,7 @@ def test2(self):
         sp.add_unit(UnitSpecies('C'))
         sp.add_unit(UnitSpecies('A'))
         self.assertEqual(sp.serial(), 'B.C.A')
-        self.assertEqual(sp.num_units(), 3)
+        self.assertEqual(len(sp.units()), 3)
 
     def test3(self):
         sp = Species('A')
@@ -47,14 +47,13 @@ def test3(self):
                 or (key == 'hoge' and value == 'hage'))
 
     def test4(self):
-        sp = Species()
-        sp.deserialize('A.B.C')
+        sp = Species('A.B.C')
         self.assertEqual(sp.serial(), 'A.B.C')
-        self.assertEqual(sp.num_units(), 3)
+        self.assertEqual(len(sp.units()), 3)
 
         sp.add_unit(UnitSpecies('D'))
         self.assertEqual(sp.serial(), 'A.B.C.D')
-        self.assertEqual(sp.num_units(), 4)
+        self.assertEqual(len(sp.units()), 4)
 
         units = sp.units()
         self.assertEqual(len(units), 4)
@@ -63,7 +62,7 @@ def test5(self):
         sp = Species('X(a,b=c^1).Y(d=e^1,f=g)')
         units = sp.units()
 
-        self.assertEqual(sp.num_units(), 2)
+        self.assertEqual(len(sp.units()), 2)
         self.assertEqual(len(units), 2)
 
         self.assertEqual(units[0].name(), 'X')