simupop-devel Mailing List for simuPOP (Page 3)

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Revision: 4965
          http://sourceforge.net/p/simupop/code/4965
Author:   bpeng2000
Date:     2015-04-21 21:37:40 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Fix a crash caused by incorrect fix of circular reference in 1.1.3 and 1.1.4

Modified Paths:
--------------
    trunk/src/utility.cpp
    trunk/src/utility.h
    trunk/test/test_03_operator.py

Modified: trunk/src/utility.cpp
===================================================================

--- trunk/src/utility.cpp	2015-04-14 04:33:16 UTC (rev 4964)
+++ trunk/src/utility.cpp	2015-04-21 21:37:40 UTC (rev 4965)
@@ -662,11 +662,12 @@
 			m_elems.push_back(defaultItems[i]);
 }
 
+
 const vectorstr & stringList::elems(const GenoStruTrait * trait) const
 {
-	if (trait == NULL || ! allAvail())
+	if (trait == NULL || !allAvail())
 		return m_elems;
-	
+
 	if (trait) {
 		if (trait->genoStruIdx() == m_trait)
 			return m_elems;
@@ -678,6 +679,7 @@
 	return m_elems;
 }
 
+
 intMatrix::intMatrix(PyObject * obj) : m_elems()
 {
 	if (obj == NULL)
@@ -835,7 +837,7 @@
 }
 
 
-pyFunc::pyFunc(PyObject * func) : m_func(func), m_numArgs(0)
+pyFunc::pyFunc(PyObject * func) : m_func(func), m_numArgs(0), m_circular(false)
 {
 	if (!m_func.isValid())
 		return;
@@ -947,10 +949,9 @@
 		// check the super class (BaseOperator) because of the SWIG
 		// interface
 		if (PyObject_HasAttrString(self, "apply") &&
-		    PyObject_HasAttrString(self, "describe")) {
-			//std::cerr << "CURCULAR " << std::endl;
-			Py_DECREF(self);
-		}
+		    PyObject_HasAttrString(self, "describe"))
+			//std::cerr << "CIRCULAR " << std::endl;
+			m_circular = true;
 		Py_DECREF(self);
 	}
 
@@ -988,14 +989,55 @@
 	}
 	Py_DECREF(co_varnames);
 	// accepting arbitrary number of parameters?
-	PyObject * co_flag = PyObject_GetAttrString(code, "co_flags");
-	DBG_ASSERT(co_flag, SystemError, "Invalid attribute co_flags for a function object");
-	m_flags = static_cast<unsigned char>(PyInt_AsLong(co_flag));
-	Py_DECREF(co_flag);
+	/*
+	   PyObject * co_flag = PyObject_GetAttrString(code, "co_flags");
+	   DBG_ASSERT(co_flag, SystemError, "Invalid attribute co_flags for a function object");
+	   int flags = static_cast<unsigned char>(PyInt_AsLong(co_flag));
+	   Py_DECREF(co_flag);
+	 */
 	Py_DECREF(code);
 }
 
 
+pyFunc::pyFunc(const pyFunc & rhs) : m_func(rhs.m_func), m_name(rhs.m_name), m_numArgs(rhs.m_numArgs),
+	m_args(rhs.m_args), m_circular(rhs.m_circular)
+{
+	// prevent reference decrease of circular reference caused by removing of
+	// temporary rhs objects
+	rhs.m_circular = false;
+}
+
+
+pyFunc & pyFunc::operator=(const pyFunc & rhs)
+{
+	m_func = rhs.m_func;
+	m_name = rhs.m_name;
+	m_numArgs = rhs.m_numArgs;
+	m_args = rhs.m_args;
+	m_circular = rhs.m_circular;
+	// prevent reference decrease of circular reference caused by removing of
+	// temporary rhs objects
+	rhs.m_circular = false;
+}
+
+
+pyFunc::~pyFunc()
+{
+	// in the case of circular reference, we will have to
+	// manually reduce reference of self, then self.func in order
+	// for both of them to be removed from memory
+	if (m_circular) {
+		PyObject * self = PyObject_GetAttrString(m_func.object(), SELF_ATTR);
+		// remove circular reference of self
+		Py_XDECREF(self);
+		// remove circular reference of self.func (not sure if this is needed)
+		Py_XDECREF(m_func.object());
+		// remove reference caused by PyObject_GetAttrString.
+		Py_XDECREF(self);
+	}
+}
+
+
 void pyGenerator::set(PyObject * gen)
 {
 	Py_XDECREF(m_iterator);

Modified: trunk/src/utility.h
===================================================================
--- trunk/src/utility.h	2015-04-14 04:33:16 UTC (rev 4964)
+++ trunk/src/utility.h	2015-04-21 21:37:40 UTC (rev 4965)
@@ -319,6 +319,12 @@
 public:
 	pyFunc(PyObject * func);
 
+	pyFunc(const pyFunc & rhs);
+
+	pyFunc & operator=(const pyFunc & rhs);
+
+	~pyFunc();
+
 	/// return number of arguments this function accepts.
 	/// This function does not count tuple parameters.
 	size_t numArgs() const
@@ -433,7 +439,10 @@
 
 	vectorstr m_args;
 
-	int m_flags;
+	// if this function is a member function of a class
+	// that release of this function requires destroying
+	// self first.
+	mutable bool m_circular;
 };
 
 /// CPPONLY

Modified: trunk/test/test_03_operator.py
===================================================================
--- trunk/test/test_03_operator.py	2015-04-14 04:33:16 UTC (rev 4964)
+++ trunk/test/test_03_operator.py	2015-04-21 21:37:40 UTC (rev 4965)
@@ -49,6 +49,16 @@
     def __call__(self, x1, x2):
         return sum([x1, x2])
 
+class OutputCollector:
+    def __init__(self):
+        self.messages = []
+
+    def func1(self, msg):
+        self.messages.append(msg)
+
+    def func2(self, msg):
+        self.messages.append(msg)
+
 class TestOperator(unittest.TestCase):
 
     def setUp(self):
@@ -217,6 +227,21 @@
             PyOutput("func2", output=func2),
         ], gen=10)
 
+
+    def testOutputMemberFunc(self):
+        '''Testing output to a function'''
+
+        simu = Simulator(Population(), rep=5)
+        o = OutputCollector()
+        # each replicate
+        simu.evolve(
+            matingScheme=CloneMating(),
+            postOps = [
+            PyOutput("func1", output=o.func1),
+            PyOutput("func2", output=o.func2),
+        ], gen=10)
+        self.assertEqual(o.messages, ['func1', 'func2'] * 50)
+
     def testOutputFileHandler(self):
         '''Testing output to a file handler'''
         simu = Simulator(Population(), rep=5)
@@ -240,7 +265,7 @@
             ], gen=10)
         with open('test1.txt') as test1txt:
             self.assertEqual(test1txt.read(), 'func2'*50)
-        #
+        # runtime error only raise in python 3
         simu = Simulator(Population(), rep=5)
         with open('test1.txt', 'wb') as out:
             # each replicate

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