ecell-cvs — CVS logs.

[Ecell-cvs] SF.net SVN: ecell:[3873] ecell3/trunk/ecell/libecs

[<mor...@us...>]

Revision: 3873
          http://ecell.svn.sourceforge.net/ecell/?rev=3873&view=rev
Author:   moriyoshi
Date:     2010-11-11 16:06:45 +0000 (Thu, 11 Nov 2010)

Log Message:
-----------
* Completely overhaul Polymorph.  It was too buggy! :(

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/Polymorph.hpp
    ecell3/trunk/ecell/libecs/tests/Polymorph_test.cpp

Modified: ecell3/trunk/ecell/libecs/Polymorph.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/Polymorph.hpp	2010-11-10 09:30:14 UTC (rev 3872)
+++ ecell3/trunk/ecell/libecs/Polymorph.hpp	2010-11-11 16:06:45 UTC (rev 3873)
@@ -116,26 +116,29 @@
             return theNumberOfItems;
         }
 
-        bool operator==( Tuple const& rhs ) const;
+        template<typename Trange>
+        bool operator==( Trange const& rhs ) const;
 
-        template< typename T_ >
-        bool operator!=( Tuple const& rhs ) const
+        template< typename Trange >
+        bool operator!=( Trange const& rhs ) const
         {
             return !operator==( rhs );
         }
 
-        bool operator<( Tuple const& rhs ) const;
+        template< typename Trange >
+        bool operator<( Trange const& rhs ) const;
 
-        template< typename T_ >
-        bool operator>=( Tuple const& rhs ) const
+        template< typename Trange >
+        bool operator>=( Trange const& rhs ) const
         {
             return !operator<( rhs );
         }
 
-        bool operator>( Tuple const& rhs ) const;
+        template< typename Trange >
+        bool operator>( Trange const& rhs ) const;
 
-        template< typename T_ >
-        bool operator<=( Tuple const& rhs ) const
+        template< typename Trange >
+        bool operator<=( Trange const& rhs ) const
         {
             return !operator<( rhs );
         }
@@ -186,16 +189,25 @@
 
         bool operator<( RawString const& rhs ) const
         {
-            size_type l( std::min( theLength, rhs.theLength ) );
-            int c( memcmp( ptr, rhs.ptr, sizeof( value_type ) * l ) );
-            return c < 0 || ( c == 0 && l == theLength );
+            size_type const l( std::min( theLength, rhs.theLength ) );
+            std::pair< value_type const*, value_type const* > c(
+                    std::mismatch( ptr, ptr + l, rhs.ptr ) );
+            return ( c.first == ptr + theLength &&
+                     c.second != rhs.ptr + rhs.theLength)
+                    || ( c.first != ptr + theLength &&
+                         c.second != rhs.ptr + rhs.theLength &&
+                         *c.first < *c.second );
         }
 
         bool operator<( const char* rhs ) const
         {
-            size_type l( std::min( theLength, std::strlen( rhs ) ) );
-            int c( memcmp( ptr, rhs, sizeof( value_type ) * l ) );
-            return c < 0 || ( c == 0 && l == theLength );
+            size_type const rl( std::strlen( rhs ) );
+            size_type const l( std::min( theLength, rl ) );
+            std::pair< value_type const*, value_type const* > c(
+                    std::mismatch( ptr, ptr + l, rhs ) );
+            return ( c.first == ptr + theLength && c.second != rhs + rl )
+                    || ( c.first != ptr + theLength &&
+                         c.second != rhs + rl && *c.first < *c.second );
         }
 
         bool operator<( String const& rhs ) const
@@ -211,16 +223,25 @@
 
         bool operator>( RawString const& rhs ) const
         {
-            size_type l( std::min( theLength, rhs.theLength ) );
-            int c( memcmp( ptr, rhs.ptr, sizeof( value_type ) * l ) );
-            return c < 0 || (c == 0 && l == theLength );
+            size_type const l( std::min( theLength, rhs.theLength ) );
+            std::pair< value_type const*, value_type const* > c(
+                    std::mismatch( ptr, ptr + l, rhs.ptr ) );
+            return ( c.first != ptr + theLength &&
+                     c.second == rhs.ptr + rhs.theLength )
+                    || ( c.first != ptr + theLength &&
+                         c.second != rhs.ptr + rhs.theLength &&
+                         *c.first > *c.second );
         }
 
         bool operator>( const char* rhs ) const
         {
-            size_type l( std::min( theLength, std::strlen( rhs ) ) );
-            int c( memcmp( ptr, rhs, sizeof( value_type ) * l ) );
-            return c < 0 || (c == 0 && l == theLength );
+            size_type const rl( std::strlen( rhs ) );
+            size_type const l( std::min( theLength, rl ) );
+            std::pair< value_type const*, value_type const* > c(
+                    std::mismatch( ptr, ptr + l, rhs ) );
+            return ( c.first != ptr + theLength && c.second == rhs + rl )
+                    || ( c.first != ptr + theLength &&
+                         c.second != rhs + rl && *c.first > *c.second );
         }
 
         bool operator>( String const& rhs ) const
@@ -246,7 +267,7 @@
 
     private:
         size_type theLength;
-        char ptr[1];
+        value_type ptr[1];
     };
 
 public:
@@ -1150,39 +1171,44 @@
 namespace libecs
 {
 
-inline bool PolymorphValue::Tuple::operator==( PolymorphValue::Tuple const& rhs ) const
+template< typename Trange >
+inline bool PolymorphValue::Tuple::operator==( Trange const& rhs ) const
 {
-    if ( theNumberOfItems != rhs.theNumberOfItems )
+    if ( theNumberOfItems != rhs.size() )
         return false;
-    return std::equal( reinterpret_cast< Polymorph const* >( ptr ),
-                       reinterpret_cast< Polymorph const* >( ptr ) + theNumberOfItems,
-                       reinterpret_cast< Polymorph const* >( rhs.ptr ) );
+    return std::equal( boost::begin( *this ), boost::end( *this ),
+                       boost::begin( rhs ) );
 }
 
-
-inline bool PolymorphValue::Tuple::operator<( PolymorphValue::Tuple const& rhs ) const
+template< typename Trange >
+inline bool PolymorphValue::Tuple::operator<( Trange const& rhs ) const
 {
-    size_type l( std::min( theNumberOfItems, rhs.theNumberOfItems ) );
-    std::pair< Polymorph const*, Polymorph const* > c(
-        std::mismatch( reinterpret_cast< Polymorph const* >( ptr ),
-                       reinterpret_cast< Polymorph const* >( ptr ) + l,
-                       reinterpret_cast< Polymorph const* >( rhs.ptr ) ) );
-    return *c.first < *c.second
-            || ( theNumberOfItems < l &&
-                 c.first == reinterpret_cast< Polymorph const * >( ptr ) + l );
+    std::pair< Polymorph const*,
+               typename boost::range_const_iterator< Trange >::type > c(
+        std::mismatch( boost::begin( *this ),
+                       boost::begin( *this )
+                           + std::min( theNumberOfItems, rhs.size() ),
+                       boost::begin( rhs ) ) );
+    return ( c.first == boost::end( *this ) && c.second != boost::end( rhs ) )
+            || ( c.first != boost::end( *this ) &&
+                 c.second != boost::end( rhs ) &&
+                 *c.first < *c.second );
 }
 
 
-inline bool PolymorphValue::Tuple::operator>( PolymorphValue::Tuple const& rhs ) const
+template< typename Trange >
+inline bool PolymorphValue::Tuple::operator>( Trange const& rhs ) const
 {
-    size_type l( std::min( theNumberOfItems, rhs.theNumberOfItems ) );
-    std::pair< Polymorph const*, Polymorph const* > c(
-        std::mismatch( reinterpret_cast< Polymorph const* >( ptr ),
-                       reinterpret_cast< Polymorph const* >( ptr ) + l,
-                       reinterpret_cast< Polymorph const* >( rhs.ptr ) ) );
-    return *c.first > *c.second
-            || ( theNumberOfItems > l &&
-                 c.second == reinterpret_cast< Polymorph const * >( rhs.ptr ) + l );
+    std::pair< Polymorph const*,
+               typename boost::range_const_iterator< Trange >::type > c(
+        std::mismatch( boost::begin( *this ),
+                       boost::begin( *this )
+                           + std::min( theNumberOfItems, rhs.size() ),
+                       boost::begin( rhs ) ) );
+    return ( c.first != boost::end( *this ) && c.second == boost::end( rhs ) )
+            || ( c.first != boost::end( *this ) &&
+                 c.second != boost::end( rhs ) &&
+                 *c.first > *c.second );
 }
 
 inline PolymorphValue::Tuple::operator Polymorph*()
@@ -1451,8 +1477,10 @@
         return false;
     case TUPLE:
         return theTupleValue == rhs;
+    case REAL:
+        return rhs.size() == 1 && theRealValue == rhs[ 0 ];
     default:
-        return rhs.size() == 1 && theRealValue == rhs[ 0 ];
+         return false;
     }
     NEVER_GET_HERE;
 }
@@ -1514,6 +1542,26 @@
     NEVER_GET_HERE;
 }
 
+inline bool PolymorphValue::operator==( PolymorphVector const& rhs ) const
+{
+    switch ( theType )
+    {
+    case NONE:
+        return false;
+    case TUPLE:
+        return theTupleValue == rhs;
+    case REAL:
+        return rhs.size() == 1 && theRealValue == rhs[ 0 ];
+    case INTEGER:
+        return rhs.size() == 1 && theIntegerValue == rhs[ 0 ];
+    case STRING:
+        return rhs.size() == 1 && theStringValue == rhs[ 0 ];
+    default:
+         return false;
+    }
+    NEVER_GET_HERE;
+}
+
 inline bool PolymorphValue::operator<( Real const& rhs ) const
 {
     switch ( theType )
@@ -1527,7 +1575,9 @@
     case STRING:
         return false;
     case TUPLE: 
-        return theTupleValue.size() < 1 || static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs;
+        return theTupleValue.size() == 0
+                || ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1545,8 +1595,9 @@
     case STRING:
         return false;
     case TUPLE: 
-        return theTupleValue.size() < 1 ||
-            static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs;
+        return theTupleValue.size() == 0
+                || ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1564,7 +1615,9 @@
     case STRING:
         return theStringValue < rhs;
     case TUPLE:
-        return theTupleValue.size() < 1 || static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs;
+        return theTupleValue.size() == 0
+                || ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1576,11 +1629,14 @@
     case NONE:
         return true;
     case REAL:
-        return rhs.size() < 1 && theRealValue < static_cast< PolymorphValue const& >( rhs[ 0 ] );
+        return ( rhs.size() == 1 && theRealValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theRealValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
     case INTEGER:
-        return rhs.size() < 1 && theIntegerValue < static_cast< PolymorphValue const& >( rhs[ 0 ] );
+        return ( rhs.size() == 1 && theIntegerValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theIntegerValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
     case STRING:
-        return rhs.size() < 1 && theStringValue < static_cast< PolymorphValue const& >( rhs[ 0 ] );
+        return ( rhs.size() == 1 && theStringValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theStringValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
     case TUPLE:
         return theTupleValue < rhs;
     }
@@ -1600,7 +1656,9 @@
     case STRING:
         return theStringValue < rhs;
     case TUPLE:
-        return theTupleValue.size() < 1 || static_cast< PolymorphValue const& >( theTupleValue[ 0 ] )< rhs;
+        return theTupleValue.size() == 0
+                || ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1618,11 +1676,34 @@
     case STRING:
         return theStringValue < rhs;
     case TUPLE:
-        return theTupleValue.size() < 1 || static_cast< PolymorphValue const& >( theTupleValue[ 0 ] )< rhs;
+        return theTupleValue.size() == 0
+                || ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) < rhs);
     }
     NEVER_GET_HERE;
 }
 
+inline bool PolymorphValue::operator<( PolymorphVector const& rhs ) const
+{
+    switch ( theType )
+    {
+    case NONE:
+        return true;
+    case REAL:
+        return ( rhs.size() == 1 && theRealValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theRealValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
+    case INTEGER:
+        return ( rhs.size() == 1 && theIntegerValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theIntegerValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
+    case STRING:
+        return ( rhs.size() == 1 && theStringValue < static_cast< PolymorphValue const& >( rhs[ 0 ] ) )
+                 || ( rhs.size() > 1 && theStringValue <= static_cast< PolymorphValue const& >( rhs[ 0 ] ) );
+    case TUPLE:
+        return theTupleValue < rhs;
+    }
+    NEVER_GET_HERE;
+}
+
 inline bool PolymorphValue::operator<( PolymorphValue const& rhs ) const
 {
     switch ( theType )
@@ -1654,8 +1735,10 @@
     case STRING:
         return true;
     case TUPLE: 
-        return theTupleValue.size() >= 1 &&
-            static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs;
+        return ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs )
+                || ( theTupleValue.size() > 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) >= rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1673,8 +1756,10 @@
     case STRING:
         return true;
     case TUPLE: 
-        return theTupleValue.size() >= 1 &&
-            static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs;
+        return ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs )
+                || ( theTupleValue.size() > 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) >= rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1692,7 +1777,10 @@
     case STRING:
         return theStringValue > rhs;
     case TUPLE:
-        return theTupleValue.size() >= 1 && static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs;
+        return ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs )
+                || ( theTupleValue.size() > 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) >= rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1705,13 +1793,13 @@
         return false;
     case REAL:
         return rhs.size() == 0
-                || ( rhs.size() == 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) < theRealValue );
+                || ( rhs.size() == 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theRealValue );
     case INTEGER:
         return rhs.size() == 0
-                || ( rhs.size() == 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) < theIntegerValue );
+                || ( rhs.size() >= 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theIntegerValue );
     case STRING:
         return rhs.size() == 0
-                || ( rhs.size() == 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] )< theStringValue );
+                || ( rhs.size() >= 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theStringValue );
     case TUPLE:
         return theTupleValue > rhs;
     }
@@ -1731,7 +1819,10 @@
     case STRING:
         return theStringValue > rhs;
     case TUPLE:
-        return theTupleValue.size() >= 1 && static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs;
+        return ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs )
+                || ( theTupleValue.size() > 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) >= rhs);
     }
     NEVER_GET_HERE;
 }
@@ -1749,11 +1840,35 @@
     case STRING:
         return theStringValue > rhs;
     case TUPLE:
-        return theTupleValue.size() >= 1 && static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs;
+        return ( theTupleValue.size() == 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) > rhs )
+                || ( theTupleValue.size() > 1 &&
+                 static_cast< PolymorphValue const& >( theTupleValue[ 0 ] ) >= rhs);
     }
     NEVER_GET_HERE;
 }
 
+inline bool PolymorphValue::operator>( PolymorphVector const& rhs ) const
+{
+    switch ( theType )
+    {
+    case NONE:
+        return false;
+    case REAL:
+        return rhs.size() == 0
+                || ( rhs.size() == 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theRealValue );
+    case INTEGER:
+        return rhs.size() == 0
+                || ( rhs.size() >= 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theIntegerValue );
+    case STRING:
+        return rhs.size() == 0
+                || ( rhs.size() >= 1 && static_cast< PolymorphValue const& >( rhs[ 0 ] ) <= theStringValue );
+    case TUPLE:
+        return theTupleValue > rhs;
+    }
+    NEVER_GET_HERE;
+}
+
 inline bool PolymorphValue::operator>( PolymorphValue const& rhs ) const
 {
     switch ( rhs.getType() )

Modified: ecell3/trunk/ecell/libecs/tests/Polymorph_test.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/tests/Polymorph_test.cpp	2010-11-10 09:30:14 UTC (rev 3872)
+++ ecell3/trunk/ecell/libecs/tests/Polymorph_test.cpp	2010-11-11 16:06:45 UTC (rev 3873)
@@ -80,3 +80,66 @@
     BOOST_CHECK_EQUAL( "1.0", Polymorph( "1.0" ) );
     BOOST_CHECK_EQUAL( Polymorph( "1.0" ), "1.0" );
 }
+
+BOOST_AUTO_TEST_CASE(testStringComparison)
+{
+    BOOST_CHECK( Polymorph( "1" ) == Polymorph( "1" ) );
+    BOOST_CHECK( Polymorph( "1" ) >= Polymorph( "1" ) );
+    BOOST_CHECK( Polymorph( "1" ) != Polymorph( "" ) );
+    BOOST_CHECK( !( Polymorph( "1" ) == Polymorph( "" ) ) );
+    BOOST_CHECK( Polymorph( "" ) != Polymorph( "1" ) );
+    BOOST_CHECK( !( Polymorph( "" ) == Polymorph( "1" ) ) );
+    BOOST_CHECK( Polymorph( "" ) < Polymorph( "1" ) );
+    BOOST_CHECK( !( Polymorph( "" ) >= Polymorph( "1" ) ) );
+    BOOST_CHECK( !( Polymorph( "" ) > Polymorph( "1" ) ) );
+    BOOST_CHECK( Polymorph( "2" ) > Polymorph( "1" ) );
+    BOOST_CHECK( !( Polymorph( "2" ) < Polymorph( "1" ) ) );
+    BOOST_CHECK( !( Polymorph( "2" ) <= Polymorph( "1" ) ) );
+    BOOST_CHECK( Polymorph( "1" ) < Polymorph( "2" ) );
+    BOOST_CHECK( !( Polymorph( "1" ) > Polymorph( "2" ) ) );
+    BOOST_CHECK( !( Polymorph( "1" ) >= Polymorph( "2" ) ) );
+    BOOST_CHECK( Polymorph( "1" ) > Polymorph( "" ) );
+    BOOST_CHECK( !( Polymorph( "1" ) < Polymorph( "" ) ) );
+    BOOST_CHECK( !( Polymorph( "1" ) <= Polymorph( "" ) ) );
+    BOOST_CHECK( Polymorph( "12" ) > Polymorph( "1" ) );
+    BOOST_CHECK( !( Polymorph( "12" ) < Polymorph( "1" ) ) );
+    BOOST_CHECK( !( Polymorph( "12" ) <= Polymorph( "1" ) ) );
+    BOOST_CHECK( Polymorph( "1" ) < Polymorph( "12" ) );
+    BOOST_CHECK( !( Polymorph( "1" ) > Polymorph( "12" ) ) );
+    BOOST_CHECK( !( Polymorph( "1" ) >= Polymorph( "12" ) ) );
+}
+
+BOOST_AUTO_TEST_CASE(testTupleComparison)
+{
+    BOOST_CHECK( Polymorph( "1" ) == Polymorph( boost::make_tuple( "1" ) ) );
+    BOOST_CHECK( Polymorph( 1l ) == Polymorph( boost::make_tuple( 1l ) ) );
+    BOOST_CHECK( Polymorph( 1.0 ) == Polymorph( boost::make_tuple( 1.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple() ) == Polymorph( boost::make_tuple() ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 1.0 ) ) == Polymorph( boost::make_tuple( 1.0 ) ) );
+
+    BOOST_CHECK( Polymorph( "1" ) != Polymorph( boost::make_tuple() ) );
+    BOOST_CHECK( Polymorph( "1" ) != Polymorph( boost::make_tuple( "2" ) ) );
+    BOOST_CHECK( Polymorph( 1l ) != Polymorph( boost::make_tuple() ) );
+    BOOST_CHECK( Polymorph( 1l ) != Polymorph( boost::make_tuple( 2l ) ) );
+    BOOST_CHECK( Polymorph( 1.0 ) != Polymorph( boost::make_tuple() ) );
+    BOOST_CHECK( Polymorph( 1.0 ) != Polymorph( boost::make_tuple( 2.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple() ) != Polymorph( boost::make_tuple( 1.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 2.0 ) ) != Polymorph( boost::make_tuple( 1.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 1.0 ) ) != Polymorph( boost::make_tuple( 1.0, 2.0 ) ) );
+
+    BOOST_CHECK( Polymorph( "1" ) < Polymorph( boost::make_tuple( "2" ) ) );
+    BOOST_CHECK( Polymorph( "1" ) < Polymorph( boost::make_tuple( "1", "2" ) ) );
+    BOOST_CHECK( Polymorph( 1l ) < Polymorph( boost::make_tuple( 2l ) ) );
+    BOOST_CHECK( Polymorph( 1l ) < Polymorph( boost::make_tuple( 1l, 2l ) ) );
+    BOOST_CHECK( Polymorph( 1.0 ) < Polymorph( boost::make_tuple( 2.0 ) ) );
+    BOOST_CHECK( Polymorph( 1.0 ) < Polymorph( boost::make_tuple( 1.0, 2.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple() ) < Polymorph( boost::make_tuple( 0.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 1.0 ) ) < Polymorph( boost::make_tuple( 1.0, 2.0 ) ) );
+
+    BOOST_CHECK( Polymorph( "2" ) > Polymorph( boost::make_tuple( "1" ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( "1", "2" ) ) > Polymorph( "1" ) );
+    BOOST_CHECK( Polymorph( 2.0 ) > Polymorph( boost::make_tuple( 1.0 ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 1.0, 2.0 ) ) > Polymorph( boost::make_tuple( 1.0 ) ) );
+    BOOST_CHECK( Polymorph( 2l ) > Polymorph( boost::make_tuple( 1l ) ) );
+    BOOST_CHECK( Polymorph( boost::make_tuple( 1l, 2l ) ) > Polymorph( boost::make_tuple( 1l ) ) );
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3872] ecell3/trunk/ecell/dm/ExpressionAssignmentProcess. cpp

[<mor...@us...>]

Revision: 3872
          http://ecell.svn.sourceforge.net/ecell/?rev=3872&view=rev
Author:   moriyoshi
Date:     2010-11-10 09:30:14 +0000 (Wed, 10 Nov 2010)

Log Message:
-----------
* Ensure ExpressionAssignmentProcess has at least one non-zero variable reference.  It would segfault before the fix.

Modified Paths:
--------------
    ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp

Modified: ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp	2010-11-05 11:27:19 UTC (rev 3871)
+++ ecell3/trunk/ecell/dm/ExpressionAssignmentProcess.cpp	2010-11-10 09:30:14 UTC (rev 3872)
@@ -101,9 +101,11 @@
         {
             if( i->getCoefficient() != 0 )
             {
-                theVariableReference = *i; 
+                theVariableReference = *i;
+                return;
             }
         }
+        THROW_EXCEPTION_INSIDE(InitializationFailed, "No variable references with non-zero coefficients exist");
     }
 
     virtual void fire()


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3871] ecell3/trunk/ecell/libecs/tests

[<mor...@us...>]

Revision: 3871
          http://ecell.svn.sourceforge.net/ecell/?rev=3871&view=rev
Author:   moriyoshi
Date:     2010-11-05 11:27:19 +0000 (Fri, 05 Nov 2010)

Log Message:
-----------
* Update testcases.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp
    ecell3/trunk/ecell/libecs/tests/VirtualMachine_test.cpp

Modified: ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp	2010-11-05 11:26:20 UTC (rev 3870)
+++ ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp	2010-11-05 11:27:19 UTC (rev 3871)
@@ -87,7 +87,7 @@
     BOOST_REQUIRE_EQUAL( op, reinterpret_cast< const scripting::InstructionHead* >(pc)->getOpcode() ); \
     if ( isReal( oper ) ) \
     { \
-        BOOST_CHECK_CLOSE_FRACTION( toReal( oper ), toReal( reinterpret_cast< const scripting::Instruction< op >* >( pc )->getOperand() ), 50 ); \
+        BOOST_CHECK_CLOSE_FRACTION( toReal( oper ), toReal( reinterpret_cast< const scripting::Instruction< op >* >( pc )->getOperand() ), .1 ); \
     } \
     else \
     { \

Modified: ecell3/trunk/ecell/libecs/tests/VirtualMachine_test.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/tests/VirtualMachine_test.cpp	2010-11-05 11:26:20 UTC (rev 3870)
+++ ecell3/trunk/ecell/libecs/tests/VirtualMachine_test.cpp	2010-11-05 11:27:19 UTC (rev 3871)
@@ -67,7 +67,7 @@
             scripting::Instruction< scripting::PUSH_REAL >( i ) );
         a.appendInstruction( scripting::Instruction< scripting::ADD >() );
         a.appendInstruction( scripting::Instruction< scripting::RET >() );
-        BOOST_CHECK_CLOSE_FRACTION( i * 2, vm.execute( *code ), 50 );
+        BOOST_CHECK_CLOSE( i * 2, vm.execute( *code ), .1 );
     }
 
     for ( Real i = 0; i < 100; i += 0.8 ) {
@@ -83,7 +83,84 @@
             scripting::Instruction< scripting::PUSH_REAL >( i ) );
         a.appendInstruction( scripting::Instruction< scripting::ADD >() );
         a.appendInstruction( scripting::Instruction< scripting::RET >() );
-        BOOST_CHECK_CLOSE_FRACTION( i * 3, vm.execute( *code ), 50 );
+        BOOST_CHECK_CLOSE( i * 3, vm.execute( *code ), .1 );
     }
 }
 
+struct Test
+{
+    Real getValue() const
+    {
+        return 4;
+    }
+};
+
+BOOST_AUTO_TEST_CASE(testFunctionCall)
+{
+    {
+        std::auto_ptr<scripting::Code> code(new scripting::Code());
+        scripting::VirtualMachine vm;
+        scripting::Assembler a( code.get() );
+        Test t;
+        a.appendInstruction(
+            scripting::Instruction< scripting::OBJECT_METHOD_REAL >(
+                scripting::RealObjectMethodProxy::createConst<
+                    Test, &Test::getValue >( &t ) ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::CALL_FUNC1 >( &std::sqrt ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 1 ) );
+        a.appendInstruction( scripting::Instruction< scripting::ADD >() );
+        a.appendInstruction( scripting::Instruction< scripting::RET >() );
+        BOOST_CHECK_CLOSE( 3, vm.execute( *code ), .1 );
+    }
+   
+    {
+        std::auto_ptr<scripting::Code> code(new scripting::Code());
+        scripting::VirtualMachine vm;
+        scripting::Assembler a( code.get() );
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 4 ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::CALL_FUNC1 >( &std::sqrt ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 1 ) );
+        a.appendInstruction( scripting::Instruction< scripting::ADD >() );
+        a.appendInstruction( scripting::Instruction< scripting::RET >() );
+        BOOST_CHECK_CLOSE( 3, vm.execute( *code ), .1 );
+    }
+
+    {
+        std::auto_ptr<scripting::Code> code(new scripting::Code());
+        scripting::VirtualMachine vm;
+        scripting::Assembler a( code.get() );
+        Test t;
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 1 ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::OBJECT_METHOD_REAL >(
+                scripting::RealObjectMethodProxy::createConst<
+                    Test, &Test::getValue >( &t ) ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::CALL_FUNC1 >( &std::sqrt ) );
+        a.appendInstruction( scripting::Instruction< scripting::ADD >() );
+        a.appendInstruction( scripting::Instruction< scripting::RET >() );
+        BOOST_CHECK_CLOSE( 3, vm.execute( *code ), .1 );
+    }
+   
+    {
+        std::auto_ptr<scripting::Code> code(new scripting::Code());
+        scripting::VirtualMachine vm;
+        scripting::Assembler a( code.get() );
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 1 ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::PUSH_REAL >( 4 ) );
+        a.appendInstruction(
+            scripting::Instruction< scripting::CALL_FUNC1 >( &std::sqrt ) );
+        a.appendInstruction( scripting::Instruction< scripting::ADD >() );
+        a.appendInstruction( scripting::Instruction< scripting::RET >() );
+        BOOST_CHECK_CLOSE( 3, vm.execute( *code ), .1 );
+    }
+}
+


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3870] ecell3/trunk/ecell/libecs/scripting/VirtualMachine .cpp

[<mor...@us...>]

Revision: 3870
          http://ecell.svn.sourceforge.net/ecell/?rev=3870&view=rev
Author:   moriyoshi
Date:     2010-11-05 11:26:20 +0000 (Fri, 05 Nov 2010)

Log Message:
-----------
* Fixed the bug that some expressions wouldn't be evaluated correctly.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/scripting/VirtualMachine.cpp

Modified: ecell3/trunk/ecell/libecs/scripting/VirtualMachine.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/scripting/VirtualMachine.cpp	2010-11-05 10:48:20 UTC (rev 3869)
+++ ecell3/trunk/ecell/libecs/scripting/VirtualMachine.cpp	2010-11-05 11:26:20 UTC (rev 3870)
@@ -96,13 +96,12 @@
     void push_back(const Telem_& elem)
     {
         *(++ptr_) = elem;
-        last = elem;
     }
 
     Telem_& pop()
     {
-        last = *(ptr_ - 1);
-        return *(ptr_--);
+        Telem_& retval(*(ptr_--));
+        return retval;
     }
 
     size_type size()
@@ -118,20 +117,23 @@
     template<size_type bkidx>
     Telem_& peek()
     {
-        if ( bkidx == 0 )
-            return last;
         return *( ptr_ - bkidx );
     }
 
+    template<size_type bkidx>
+    Telem_ const& peek() const
+    {
+        return *( ptr_ - bkidx );
+    }
+
     void pop_back()
     {
-        last = *(--ptr_);
+        --ptr_;
     }
 
 private:
     Telem_ elems_[ maxdepth_ + 1 ];
     Telem_* ptr_;
-    Telem_ last;
 };
 
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3869] ecell3/trunk/ecell/libecs/tests/ ExpressionCompiler_test.cpp

[<mor...@us...>]

Revision: 3869
          http://ecell.svn.sourceforge.net/ecell/?rev=3869&view=rev
Author:   moriyoshi
Date:     2010-11-05 10:48:20 +0000 (Fri, 05 Nov 2010)

Log Message:
-----------
* Fix test case.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp

Modified: ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp	2010-09-27 07:46:09 UTC (rev 3868)
+++ ecell3/trunk/ecell/libecs/tests/ExpressionCompiler_test.cpp	2010-11-05 10:48:20 UTC (rev 3869)
@@ -394,7 +394,7 @@
         CHECK_INSTRUCTION( pc, scripting::LOAD_REAL, &aPropertyAccess.a );
         CHECK_INSTRUCTION( pc, scripting::ADD, scripting::NoOperand() );
         CHECK_INSTRUCTION( pc, scripting::OBJECT_METHOD_REAL, (
-                scripting::RealObjectMethodProxy::create<
+                scripting::RealObjectMethodProxy::createConst<
                     Variable, &Variable::getValue >( 0 ) ) );
         CHECK_INSTRUCTION( pc, scripting::ADD, scripting::NoOperand() );
         CHECK_INSTRUCTION( pc, scripting::RET, scripting::NoOperand() );
@@ -410,4 +410,83 @@
     }
 }
 
+BOOST_AUTO_TEST_CASE(testFunctionCall)
+{
+    class ErrorReporter: public scripting::ErrorReporter {
+    public:
+        ErrorReporter() {}
 
+        virtual void error( const String& type, const String& msg ) const {
+            throw type;
+        }
+    } anErrorReporter;
+
+    class PropertyAccess: public scripting::PropertyAccess {
+    public:
+        PropertyAccess()
+            : a(0), b(0), c(0)
+        {
+        }
+
+        virtual Real* get( const String& name ) {
+            if (name == "a") {
+                return &a;
+            } else if (name == "b") {
+                return &b;
+            } else if (name == "c") {
+                return &c;
+            }
+            return 0;
+        }
+    public:
+        Real a, b, c;
+    } aPropertyAccess;
+
+    class VariableReferenceResolver: public scripting::VariableReferenceResolver {
+    public:
+        virtual const VariableReference* get(
+                const String& name ) const
+        {
+            if (name == "A") {
+                return &a;
+            } else if (name == "B") {
+                return &b;
+            } else if (name == "C") {
+                return &c;
+            }
+            return 0;
+        }
+    public:
+        VariableReference a, b, c;
+    } aVarRefResolver;
+
+
+    class EntityResolver: public scripting::EntityResolver {
+    public:
+        virtual Entity* get( const String& name )
+        {
+            return 0;
+        }
+    } anEntityResolver;
+
+    scripting::ExpressionCompiler ec(
+        anErrorReporter, aPropertyAccess,
+        anEntityResolver, aVarRefResolver );
+
+    {
+        std::auto_ptr<const scripting::Code> code(
+             ec.compileExpression("sqrt( A.Value ) + 1.0") );
+
+        const unsigned char* pc = code->data();
+        const unsigned char* eoc = &*code->end();
+        CHECK_INSTRUCTION( pc, scripting::OBJECT_METHOD_REAL, (
+                scripting::RealObjectMethodProxy::createConst<
+                    Variable, &Variable::getValue >( 0 ) ) );
+        CHECK_INSTRUCTION( pc, scripting::CALL_FUNC1,
+                static_cast< double(*)( double ) >( &std::sqrt ) );
+        CHECK_INSTRUCTION( pc, scripting::PUSH_REAL, 1 );
+        CHECK_INSTRUCTION( pc, scripting::ADD, scripting::NoOperand() );
+        CHECK_INSTRUCTION( pc, scripting::RET, scripting::NoOperand() );
+        BOOST_CHECK_EQUAL(eoc, pc);
+    }
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3868] ecell3/trunk/doc/users-manual/Makefile.am

[<mor...@us...>]

Revision: 3868
          http://ecell.svn.sourceforge.net/ecell/?rev=3868&view=rev
Author:   moriyoshi
Date:     2010-09-27 07:46:09 +0000 (Mon, 27 Sep 2010)

Log Message:
-----------
* Fix install rule so it fits to docbook to html converters that generate
  nested directories under the output directory.

Modified Paths:
--------------
    ecell3/trunk/doc/users-manual/Makefile.am

Modified: ecell3/trunk/doc/users-manual/Makefile.am
===================================================================
--- ecell3/trunk/doc/users-manual/Makefile.am	2010-09-22 17:06:13 UTC (rev 3867)
+++ ecell3/trunk/doc/users-manual/Makefile.am	2010-09-27 07:46:09 UTC (rev 3868)
@@ -3,9 +3,6 @@
 DOC_pdf = users-manual.pdf
 DOC_dvi = users-manual.dvi
 
-_htmldir = $(htmldir)/$(DOC_html)
-_html_DATA = $(DOC_html)/*
-
 if BUILD_USERS_MANUAL_html
 $(DOC_html)/*: users-manual.xml
 	$(DB2HTML) -o $(DOC_html) $<
@@ -56,6 +53,20 @@
 EXTRA_DIST += $(DOC_html)
 endif
 
+if BUILD_USERS_MANUAL_html
+install-data-local:
+	(cd "$(DOC_html)" && \
+	find . -type d | while read path; do $(INSTALL) -d "$(DESTDIR)$(htmldir)/$(DOC_html)/$$path"; done && \
+	find . -type f | while read path; do $(INSTALL) -m 644 $$path "$(DESTDIR)$(htmldir)/$(DOC_html)/$$path"; done)
+
+uninstall-local:
+	( cd "$(DESTDIR)$(htmldir)" && rm -rf "$(DOC_html)" )
+else
+install-data-local:
+
+uninstall-local:
+endif
+
 clean-local:
 	$(RM) -f $(DOC_ps) $(DOC_pdf) $(DOC_dvi)
 	$(RM) -rf *.junk *.tex


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3867] ecell3/trunk/NEWS

[<mor...@us...>]

Revision: 3867
          http://ecell.svn.sourceforge.net/ecell/?rev=3867&view=rev
Author:   moriyoshi
Date:     2010-09-22 17:06:13 +0000 (Wed, 22 Sep 2010)

Log Message:
-----------
* Give a go for .2.1.

Modified Paths:
--------------
    ecell3/trunk/NEWS

Modified: ecell3/trunk/NEWS
===================================================================
--- ecell3/trunk/NEWS	2010-09-22 17:05:28 UTC (rev 3866)
+++ ecell3/trunk/NEWS	2010-09-22 17:06:13 UTC (rev 3867)
@@ -1,4 +1,4 @@
-ecell-3.2.1: ?-Jul-2010
+ecell-3.2.1: 23-Sep-2010
 
  * Fix segmentation fault in PythonProcess and PythonFluxProcess.
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3866] ecell3/trunk/ecell/libecs/MethodProxy.hpp

[<mor...@us...>]

Revision: 3866
          http://ecell.svn.sourceforge.net/ecell/?rev=3866&view=rev
Author:   moriyoshi
Date:     2010-09-22 17:05:28 +0000 (Wed, 22 Sep 2010)

Log Message:
-----------
* Workaround for the bug in GCC 4.4

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/MethodProxy.hpp

Modified: ecell3/trunk/ecell/libecs/MethodProxy.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-22 13:43:35 UTC (rev 3865)
+++ ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-22 17:05:28 UTC (rev 3866)
@@ -65,7 +65,7 @@
     template< RET (CLASS::*METHOD)() const >
     static MethodProxy createConst()
     {
-        return MethodProxy( reinterpret_cast< Invoker >( &invokeConst<METHOD> ) );
+        return MethodProxy( &invokeConst<METHOD> );
     }
 
     inline bool operator==( MethodProxy const& that ) const
@@ -93,7 +93,7 @@
     }
 
     template< RET (CLASS::*METHOD)() const >
-    inline static RET invokeConst( CLASS const* anObject )
+    inline static RET invokeConst( CLASS* anObject )
     {
         return ( anObject->*METHOD )();
     }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3865] ecell-build/trunk/pkg/rpm

[<mor...@us...>]

Revision: 3865
          http://ecell.svn.sourceforge.net/ecell/?rev=3865&view=rev
Author:   moriyoshi
Date:     2010-09-22 13:43:35 +0000 (Wed, 22 Sep 2010)

Log Message:
-----------
* Update.

Modified Paths:
--------------
    ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch
    ecell-build/trunk/pkg/rpm/ecell3.spec

Modified: ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch
===================================================================
--- ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch	2010-09-17 04:54:53 UTC (rev 3864)
+++ ecell-build/trunk/pkg/rpm/ecell-3.2.1-ply-2.3-compat.patch	2010-09-22 13:43:35 UTC (rev 3865)
@@ -8,7 +8,7 @@
 -    lex.lex( lextab=lextabmod[-1], optimize=1, outputdir=os.path.join( outputdir,*lextabmod[:-1] ) )
 -    yacc.yacc( tabmodule=parsertabmod[-1], outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
 +    lex.lex( lextab=lextabmod[-1], optimize=1 )
-+    os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) )
++    os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) + ".py" )
 +    yacc.yacc( tabmodule=parsertabmod[-1], optimize=1, outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
  
  def convertEm2Eml( anEmFileObject, debug=0 ):
@@ -23,7 +23,7 @@
 -    lex.lex( lextab=lextabmod[-1], optimize=1, outputdir=os.path.join( outputdir,*lextabmod[:-1] ) )
 -    yacc.yacc( tabmodule=parsertabmod[-1], outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
 +    lex.lex( lextab=lextabmod[-1], optimize=1 )
-+    os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) )
++    os.rename( lextabmod[-1] + ".py", os.path.join( outputdir, *lextabmod ) + ".py" )
 +    yacc.yacc( tabmodule=parsertabmod[-1], optimize=1, outputdir=os.path.join( outputdir, *parsertabmod[:-1] ) )
  
  

Modified: ecell-build/trunk/pkg/rpm/ecell3.spec
===================================================================
--- ecell-build/trunk/pkg/rpm/ecell3.spec	2010-09-17 04:54:53 UTC (rev 3864)
+++ ecell-build/trunk/pkg/rpm/ecell3.spec	2010-09-22 13:43:35 UTC (rev 3865)
@@ -20,6 +20,7 @@
 Requires: python-ply >= 2.3
 Requires: glibc
 BuildRequires: make
+BuildRequires: numpy >= 1.0.3
 BuildRequires: python-devel
 BuildRequires: pygtk2 >= 2.4
 BuildRequires: python-ply >= 2.3
@@ -112,12 +113,13 @@
     infodir=%{_infodir} \
     docdir=%{_datadir}/doc/ecell3 \
     install
-rm -rf ${RPM_BUILD_ROOT}/usr/lib/python*
+# rm -rf ${RPM_BUILD_ROOT}/usr/lib/python*
 mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/users-manual .
 mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/api .
 mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/model-editor .
 mv ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3/samples .
 rm -rf ${RPM_BUILD_ROOT}%{_datadir}/doc/ecell3
+find ${RPM_BUILD_ROOT}%{_libdir} -name "*.out" -a -type f | xargs rm -f
 
 %clean
 rm -rf ${RPM_BUILD_ROOT}
@@ -135,10 +137,13 @@
 %{_libdir}/libecs.so.*
 %{_libdir}/libemc.so.*
 %{_libdir}/ecell-3.2/dms
-%{_libdir}/python*
-%ifarch x86_64 ppc64 sparc64
-%{python_sitelib}/*
-%endif
+%{_libdir}/python*/site-packages/ecell/*.so
+%{_libdir}/python*/site-packages/ecell/*.py
+%{_libdir}/python*/site-packages/ecell/*.pyc
+%{_libdir}/python*/site-packages/ecell/analysis
+%{_libdir}/python*/site-packages/ecell/session_manager
+%{python_sitelib}/ecell/ui/__init__.py
+%{python_sitelib}/ecell/ui/__init__.pyc
 
 %files devel
 %defattr(-,root,root)
@@ -160,6 +165,7 @@
 %{_bindir}/ecell3-session-monitor
 %{_libdir}/ecell-3.2/session-monitor
 %{_datadir}/ecell-3.2/session-monitor
+%{python_sitelib}/ecell/ui/osogo
 
 %files model-editor
 %defattr(-,root,root)
@@ -168,6 +174,7 @@
 %{_bindir}/ecell3-model-editor
 %{_libdir}/ecell-3.2/model-editor
 %{_datadir}/ecell-3.2/model-editor
+%{python_sitelib}/ecell/ui/model_editor
 
 %changelog
 * Wed Jun 30 2010 Moriyoshi Koizumi <mo...@ri...>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3864] ecell3/trunk/ecell/pyecell/ecell/analysis/ emlsupport.py

[<ka...@us...>]

Revision: 3864
          http://ecell.svn.sourceforge.net/ecell/?rev=3864&view=rev
Author:   kaizu
Date:     2010-09-17 04:54:53 +0000 (Fri, 17 Sep 2010)

Log Message:
-----------
os.chdir was removed

Modified Paths:
--------------
    ecell3/trunk/ecell/pyecell/ecell/analysis/emlsupport.py

Modified: ecell3/trunk/ecell/pyecell/ecell/analysis/emlsupport.py
===================================================================
--- ecell3/trunk/ecell/pyecell/ecell/analysis/emlsupport.py	2010-09-14 10:14:39 UTC (rev 3863)
+++ ecell3/trunk/ecell/pyecell/ecell/analysis/emlsupport.py	2010-09-17 04:54:53 UTC (rev 3864)
@@ -131,7 +131,6 @@
 
         if type( fileName ) == str:
             self.__theEmlFileName = os.path.abspath( fileName )
-            os.chdir( os.path.dirname( self.getEmlFileName() ) )
         else:
             raise TypeError, ' The type of fileName must be string (file name) '
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3863] ecell3/trunk/ecell/libecs/MethodProxy.hpp

[<mor...@us...>]

Revision: 3863
          http://ecell.svn.sourceforge.net/ecell/?rev=3863&view=rev
Author:   moriyoshi
Date:     2010-09-14 10:14:39 +0000 (Tue, 14 Sep 2010)

Log Message:
-----------
* Fix weird bug caused by gcc's wrong function resolution.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/MethodProxy.hpp

Modified: ecell3/trunk/ecell/libecs/MethodProxy.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-14 10:13:42 UTC (rev 3862)
+++ ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-14 10:14:39 UTC (rev 3863)
@@ -43,7 +43,7 @@
 class MethodProxy<CLASS, RET>
 {
 private:
-    typedef RET (* Invoker )( CLASS* );
+    typedef RET ( *Invoker )( CLASS* );
 
 public:
     RET operator()( CLASS* anObject ) const 
@@ -110,7 +110,7 @@
 class ObjectMethodProxy<RET>
 {
 private:
-    typedef RET (* Invoker )( void* );
+    typedef RET ( *Invoker )( void* );
 
 public:
     RET operator()() const 
@@ -121,13 +121,13 @@
 	template < typename T, RET (T::*TMethod)() >
     static ObjectMethodProxy create( T* anObject )
     {
-        return ObjectMethodProxy( reinterpret_cast< Invoker >( &invoke< T, TMethod > ), anObject );
+        return ObjectMethodProxy( &invoke< T, TMethod >, anObject );
     }
 
 	template < typename T, RET (T::*TMethod)() const >
     static ObjectMethodProxy createConst( T const* anObject )
     {
-        return ObjectMethodProxy( reinterpret_cast< Invoker >( &invokeConst< T, TMethod > ), const_cast< T* >( anObject ) );
+        return ObjectMethodProxy( &invokeConst< T, TMethod >, const_cast< T* >( anObject ) );
     }
 
 	inline bool operator==( ObjectMethodProxy const& that ) const
@@ -151,15 +151,15 @@
     }
 
     template < class T, RET (T::*TMethod)() >
-    static RET invoke( T* anObject )
+    static RET invoke( void* anObject )
     {
-        return ( anObject->*TMethod )();
+        return ( reinterpret_cast< T* >( anObject )->*TMethod )();
     }
 
     template < class T, RET (T::*TMethod)() const >
-    static RET invokeConst( T const* anObject )
+    static RET invokeConst( void* anObject )
     {
-        return ( anObject->*TMethod )();
+        return ( reinterpret_cast< T const* >( anObject )->*TMethod )();
     }
 
 private:


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3862] ecell3/trunk/ecell/libecs/System.hpp

[<mor...@us...>]

Revision: 3862
          http://ecell.svn.sourceforge.net/ecell/?rev=3862&view=rev
Author:   moriyoshi
Date:     2010-09-14 10:13:42 +0000 (Tue, 14 Sep 2010)

Log Message:
-----------
* Remove redundant typename ;)

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/System.hpp

Modified: ecell3/trunk/ecell/libecs/System.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/System.hpp	2010-09-09 02:47:22 UTC (rev 3861)
+++ ecell3/trunk/ecell/libecs/System.hpp	2010-09-14 10:13:42 UTC (rev 3862)
@@ -295,19 +295,19 @@
 
 
 template <>
-inline typename System::Variables System::getEntities< Variable >() const
+inline System::Variables System::getEntities< Variable >() const
 {
     return getVariables();
 }
 
 template <>
-inline typename System::Processes System::getEntities< Process >() const
+inline System::Processes System::getEntities< Process >() const
 {
     return getProcesses();
 }
 
 template <>
-inline typename System::Systems   System::getEntities< System >() const
+inline System::Systems   System::getEntities< System >() const
 {
     return getSystems();
 }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3861] ecell3/trunk/ecell/dm

[<mor...@us...>]

Revision: 3861
          http://ecell.svn.sourceforge.net/ecell/?rev=3861&view=rev
Author:   moriyoshi
Date:     2010-09-09 02:47:22 +0000 (Thu, 09 Sep 2010)

Log Message:
-----------
* Add missing DM_IF

Modified Paths:
--------------
    ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
    ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp

Modified: ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp	2010-09-09 02:46:22 UTC (rev 3860)
+++ ecell3/trunk/ecell/dm/ESSYNSProcessInterface.hpp	2010-09-09 02:47:22 UTC (rev 3861)
@@ -31,7 +31,7 @@
 
 #include <libecs/libecs.hpp>
 
-struct ESSYNSProcessInterface
+struct DM_IF ESSYNSProcessInterface
 {
     virtual const boost::multi_array< libecs::Real, 2 >& getESSYNSMatrix() = 0;
 

Modified: ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp	2010-09-09 02:46:22 UTC (rev 3860)
+++ ecell3/trunk/ecell/dm/GillespieProcessInterface.hpp	2010-09-09 02:47:22 UTC (rev 3861)
@@ -30,7 +30,7 @@
 
 #include <libecs/libecs.hpp>
 
-struct GillespieProcessInterface
+struct DM_IF GillespieProcessInterface
 {
     virtual GET_METHOD( libecs::Real, Propensity ) = 0;
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3860] ecell3/trunk/ecell/dm/GillespieProcess.cpp

[<mor...@us...>]

Revision: 3860
          http://ecell.svn.sourceforge.net/ecell/?rev=3860&view=rev
Author:   moriyoshi
Date:     2010-09-09 02:46:22 +0000 (Thu, 09 Sep 2010)

Log Message:
-----------
* MSVC fix.

Modified Paths:
--------------
    ecell3/trunk/ecell/dm/GillespieProcess.cpp

Modified: ecell3/trunk/ecell/dm/GillespieProcess.cpp
===================================================================
--- ecell3/trunk/ecell/dm/GillespieProcess.cpp	2010-09-09 02:45:46 UTC (rev 3859)
+++ ecell3/trunk/ecell/dm/GillespieProcess.cpp	2010-09-09 02:46:22 UTC (rev 3860)
@@ -33,10 +33,10 @@
     : theOrder( 0 ),
       c( 0.0 ),
       theGetPropensityMethodPtr(
-              RealMethodProxy::create<
+              RealMethodProxy::createConst<
                       &GillespieProcess::getZero>() ),
       theGetMinValueMethodPtr(
-              RealMethodProxy::create<
+              RealMethodProxy::createConst<
                       &GillespieProcess::getZero>() ),
       theGetPDMethodPtr( &GillespieProcess::getPD_Zero )
 {
@@ -310,35 +310,35 @@
     if( theOrder == 0 )     // no substrate
     {
         theGetPropensityMethodPtr =
-                    RealMethodProxy::create<&GillespieProcess::getZero>();
+                    RealMethodProxy::createConst<&GillespieProcess::getZero>();
         theGetMinValueMethodPtr   =
-                    RealMethodProxy::create<&GillespieProcess::getZero>();
+                    RealMethodProxy::createConst<&GillespieProcess::getZero>();
         theGetPDMethodPtr         = &GillespieProcess::getPD_Zero;
     }
     else if( theOrder == 1 )     // one substrate, first order.
     {
         theGetPropensityMethodPtr =
-                    RealMethodProxy::create<&GillespieProcess::getPropensity_FirstOrder>();
+                    RealMethodProxy::createConst<&GillespieProcess::getPropensity_FirstOrder>();
         theGetMinValueMethodPtr   =
-                    RealMethodProxy::create<&GillespieProcess::getMinValue_FirstOrder>();
+                    RealMethodProxy::createConst<&GillespieProcess::getMinValue_FirstOrder>();
         theGetPDMethodPtr         = &GillespieProcess::getPD_FirstOrder;
     }
     else if( theOrder == 2 )
     {
         if( getZeroVariableReferenceOffset() == 2 ) // 2 substrates, 2nd order
         {    
-            theGetPropensityMethodPtr   = RealMethodProxy::create<
+            theGetPropensityMethodPtr   = RealMethodProxy::createConst<
                     &GillespieProcess::getPropensity_SecondOrder_TwoSubstrates > ();
-            theGetMinValueMethodPtr     = RealMethodProxy::create<
+            theGetMinValueMethodPtr     = RealMethodProxy::createConst<
                     &GillespieProcess::getMinValue_SecondOrder_TwoSubstrates >();
             theGetPDMethodPtr           =
                     &GillespieProcess::getPD_SecondOrder_TwoSubstrates;
         }
         else // one substrate, second order (coeff == -2)
         {
-            theGetPropensityMethodPtr = RealMethodProxy::create<
+            theGetPropensityMethodPtr = RealMethodProxy::createConst<
                     &GillespieProcess::getPropensity_SecondOrder_OneSubstrate>();
-            theGetMinValueMethodPtr   = RealMethodProxy::create<
+            theGetMinValueMethodPtr   = RealMethodProxy::createConst<
                     &GillespieProcess::getMinValue_SecondOrder_OneSubstrate>();
             theGetPDMethodPtr         =
                     &GillespieProcess::getPD_SecondOrder_OneSubstrate;
@@ -347,9 +347,9 @@
     else
     {
         //FIXME: generic functions should come here.
-        theGetPropensityMethodPtr = RealMethodProxy::create<
+        theGetPropensityMethodPtr = RealMethodProxy::createConst<
                 &GillespieProcess::getZero>();
-        theGetPropensityMethodPtr = RealMethodProxy::create<
+        theGetPropensityMethodPtr = RealMethodProxy::createConst<
                 &GillespieProcess::getZero>();
         theGetPDMethodPtr         = &GillespieProcess::getPD_Zero;
     }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3859] ecell3/trunk/ecell/libecs/MethodProxy.hpp

[<mor...@us...>]

Revision: 3859
          http://ecell.svn.sourceforge.net/ecell/?rev=3859&view=rev
Author:   moriyoshi
Date:     2010-09-09 02:45:46 +0000 (Thu, 09 Sep 2010)

Log Message:
-----------
* More MSVC fixes...

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/MethodProxy.hpp

Modified: ecell3/trunk/ecell/libecs/MethodProxy.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-09 02:44:56 UTC (rev 3858)
+++ ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-09 02:45:46 UTC (rev 3859)
@@ -63,9 +63,9 @@
     }
 
     template< RET (CLASS::*METHOD)() const >
-    static MethodProxy create()
+    static MethodProxy createConst()
     {
-        return MethodProxy( &invoke<METHOD> );
+        return MethodProxy( reinterpret_cast< Invoker >( &invokeConst<METHOD> ) );
     }
 
     inline bool operator==( MethodProxy const& that ) const
@@ -93,7 +93,7 @@
     }
 
     template< RET (CLASS::*METHOD)() const >
-    inline static RET invoke( CLASS* anObject )
+    inline static RET invokeConst( CLASS const* anObject )
     {
         return ( anObject->*METHOD )();
     }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3858] ecell3/trunk/ecell/libemc/SimulatorImplementation. hpp

[<mor...@us...>]

Revision: 3858
          http://ecell.svn.sourceforge.net/ecell/?rev=3858&view=rev
Author:   moriyoshi
Date:     2010-09-09 02:44:56 +0000 (Thu, 09 Sep 2010)

Log Message:
-----------
* Remove unwanted consts.

Modified Paths:
--------------
    ecell3/trunk/ecell/libemc/SimulatorImplementation.hpp

Modified: ecell3/trunk/ecell/libemc/SimulatorImplementation.hpp
===================================================================
--- ecell3/trunk/ecell/libemc/SimulatorImplementation.hpp	2010-09-08 13:39:18 UTC (rev 3857)
+++ ecell3/trunk/ecell/libemc/SimulatorImplementation.hpp	2010-09-09 02:44:56 UTC (rev 3858)
@@ -169,13 +169,13 @@
 
     virtual libecs::Polymorph getNextEvent() const = 0;
 
-    virtual void step( const libecs::Integer aNumSteps ) = 0;
+    virtual void step( libecs::Integer aNumSteps ) = 0;
 
     virtual libecs::Real getCurrentTime() const = 0;
 
     virtual void run() = 0;
 
-    virtual void run( const libecs::Real aDuration ) = 0;
+    virtual void run( libecs::Real aDuration ) = 0;
 
     virtual void stop() = 0;
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3857] ecell3/trunk/ecell/libecs/System.hpp

[<mor...@us...>]

Revision: 3857
          http://ecell.svn.sourceforge.net/ecell/?rev=3857&view=rev
Author:   moriyoshi
Date:     2010-09-08 13:39:18 +0000 (Wed, 08 Sep 2010)

Log Message:
-----------
* Remove usage of DECLARE_MAP()
* Add missing typenames to dependent names.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/System.hpp

Modified: ecell3/trunk/ecell/libecs/System.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/System.hpp	2010-09-08 13:38:16 UTC (rev 3856)
+++ ecell3/trunk/ecell/libecs/System.hpp	2010-09-08 13:39:18 UTC (rev 3857)
@@ -48,9 +48,9 @@
 {
 public:
     // Maps used for entry lists
-    typedef std::map<String, Variable*, std::less<String> > VariableMap;
-    typedef std::map<String, Process*, std::less<String> > ProcessMap;
-    typedef std::map<String, System*, std::less<String> > SystemMap;
+    typedef std::map< String, Variable*, std::less< String > > VariableMap;
+    typedef std::map< String, Process*, std::less< String > > ProcessMap;
+    typedef std::map< String, System*, std::less< String > > SystemMap;
 
     typedef boost::iterator_range< VariableMap::iterator > Variables;
     typedef boost::iterator_range< ProcessMap::iterator > Processes;
@@ -121,7 +121,7 @@
     }
 
     template <class T_>
-    boost::iterator_range< typename std::map< const String, T_*, std::less<const String> >::iterator > getEntities() const;
+    boost::iterator_range< typename std::map< String, T_*, std::less< String > >::iterator > getEntities() const;
 
     Variables getVariables() const
     {
@@ -295,19 +295,19 @@
 
 
 template <>
-inline System::Variables System::getEntities< Variable >() const
+inline typename System::Variables System::getEntities< Variable >() const
 {
     return getVariables();
 }
 
 template <>
-inline System::Processes System::getEntities< Process >() const
+inline typename System::Processes System::getEntities< Process >() const
 {
     return getProcesses();
 }
 
 template <>
-inline System::Systems   System::getEntities< System >() const
+inline typename System::Systems   System::getEntities< System >() const
 {
     return getSystems();
 }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3856] ecell3/trunk/ecell/libecs

[<mor...@us...>]

Revision: 3856
          http://ecell.svn.sourceforge.net/ecell/?rev=3856&view=rev
Author:   moriyoshi
Date:     2010-09-08 13:38:16 +0000 (Wed, 08 Sep 2010)

Log Message:
-----------
* MSVC cannot gracefully handle template overloaded functions with a function pointer as its template argument.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/MethodProxy.hpp
    ecell3/trunk/ecell/libecs/scripting/Assembler.cpp

Modified: ecell3/trunk/ecell/libecs/MethodProxy.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-08 10:47:26 UTC (rev 3855)
+++ ecell3/trunk/ecell/libecs/MethodProxy.hpp	2010-09-08 13:38:16 UTC (rev 3856)
@@ -118,19 +118,19 @@
         return theInvoker( theObject ); 
     }
 
-    template < class T, RET (T::*TMethod)() >
+	template < typename T, RET (T::*TMethod)() >
     static ObjectMethodProxy create( T* anObject )
     {
-        return ObjectMethodProxy( &invoke<T,TMethod>, anObject );
+        return ObjectMethodProxy( reinterpret_cast< Invoker >( &invoke< T, TMethod > ), anObject );
     }
 
-    template < class T, RET (T::*TMethod)() const >
-    static ObjectMethodProxy create( T* anObject )
+	template < typename T, RET (T::*TMethod)() const >
+    static ObjectMethodProxy createConst( T const* anObject )
     {
-        return ObjectMethodProxy( &invoke<T,TMethod>, anObject );
+        return ObjectMethodProxy( reinterpret_cast< Invoker >( &invokeConst< T, TMethod > ), const_cast< T* >( anObject ) );
     }
 
-    inline bool operator==( ObjectMethodProxy const& that ) const
+	inline bool operator==( ObjectMethodProxy const& that ) const
     {
         return that.theInvoker == theInvoker;
     }
@@ -151,15 +151,15 @@
     }
 
     template < class T, RET (T::*TMethod)() >
-    static RET invoke( void* anObject )
+    static RET invoke( T* anObject )
     {
-        return ( static_cast<T*>(anObject)->*TMethod )();
+        return ( anObject->*TMethod )();
     }
 
     template < class T, RET (T::*TMethod)() const >
-    static RET invoke( void* anObject )
+    static RET invokeConst( T const* anObject )
     {
-        return ( static_cast<T const*>(anObject)->*TMethod )();
+        return ( anObject->*TMethod )();
     }
 
 private:

Modified: ecell3/trunk/ecell/libecs/scripting/Assembler.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/scripting/Assembler.cpp	2010-09-08 10:47:26 UTC (rev 3855)
+++ ecell3/trunk/ecell/libecs/scripting/Assembler.cpp	2010-09-08 13:38:16 UTC (rev 3856)
@@ -41,14 +41,14 @@
  appendInstruction\
    ( Instruction<OBJECT_METHOD_REAL>\
      ( RealObjectMethodProxy::\
-       create< CLASSNAME, & CLASSNAME::METHODNAME >\
+       createConst< CLASSNAME, & CLASSNAME::METHODNAME >\
        ( OBJECT ) ) ) // \
  
 #define APPEND_OBJECT_METHOD_INTEGER( OBJECT, CLASSNAME, METHODNAME )\
  appendInstruction\
    ( Instruction<OBJECT_METHOD_INTEGER>\
      ( IntegerObjectMethodProxy::\
-       create< CLASSNAME, & CLASSNAME::METHODNAME >\
+       createConst< CLASSNAME, & CLASSNAME::METHODNAME >\
        ( OBJECT ) ) ) // \
  
 void


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3855] ecell3/trunk/ecell/libecs

[<mor...@us...>]

Revision: 3855
          http://ecell.svn.sourceforge.net/ecell/?rev=3855&view=rev
Author:   moriyoshi
Date:     2010-09-08 10:47:26 +0000 (Wed, 08 Sep 2010)

Log Message:
-----------
* Fix Stepper so that setStepInterval() can be overridden in the subclass.

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/DifferentialStepper.cpp
    ecell3/trunk/ecell/libecs/DifferentialStepper.hpp
    ecell3/trunk/ecell/libecs/Stepper.cpp
    ecell3/trunk/ecell/libecs/Stepper.hpp

Modified: ecell3/trunk/ecell/libecs/DifferentialStepper.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/DifferentialStepper.cpp	2010-09-08 08:56:43 UTC (rev 3854)
+++ ecell3/trunk/ecell/libecs/DifferentialStepper.cpp	2010-09-08 10:47:26 UTC (rev 3855)
@@ -407,5 +407,11 @@
     return new DifferentialStepper::Interpolant( aVariable, this );
 }
 
+SET_METHOD_DEF( Real, StepInterval, DifferentialStepper )
+{
+    Stepper::setStepInterval( value );
+    setTolerableStepInterval( value );
+    setNextStepInterval( value );
+}
 
 } // namespace libecs

Modified: ecell3/trunk/ecell/libecs/DifferentialStepper.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/DifferentialStepper.hpp	2010-09-08 08:56:43 UTC (rev 3854)
+++ ecell3/trunk/ecell/libecs/DifferentialStepper.hpp	2010-09-08 10:47:26 UTC (rev 3855)
@@ -36,6 +36,7 @@
 #include "libecs/Stepper.hpp"
 
 #include <boost/multi_array.hpp>
+#include <iostream>
 
 namespace libecs
 {
@@ -114,12 +115,7 @@
         return theTolerableStepInterval;
     }
 
-    virtual void setStepInterval( Real aStepInterval )
-    {
-        Stepper::setStepInterval( aStepInterval );
-        setTolerableStepInterval( aStepInterval );
-        setNextStepInterval( aStepInterval );
-    }
+    virtual SET_METHOD( Real, StepInterval );
 
     void resetAll();
 

Modified: ecell3/trunk/ecell/libecs/Stepper.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/Stepper.cpp	2010-09-08 08:56:43 UTC (rev 3854)
+++ ecell3/trunk/ecell/libecs/Stepper.cpp	2010-09-08 10:47:26 UTC (rev 3855)
@@ -572,6 +572,10 @@
     }
 }
 
+SET_METHOD_DEF( Real, StepInterval, Stepper )
+{
+    setNextTime( getCurrentTime() + value );
+}
 
 SET_METHOD_DEF( String, RngSeed, Stepper )
 {

Modified: ecell3/trunk/ecell/libecs/Stepper.hpp
===================================================================
--- ecell3/trunk/ecell/libecs/Stepper.hpp	2010-09-08 08:56:43 UTC (rev 3854)
+++ ecell3/trunk/ecell/libecs/Stepper.hpp	2010-09-08 10:47:26 UTC (rev 3855)
@@ -146,7 +146,7 @@
 
        @return the step interval of this Stepper
     */
-    virtual GET_METHOD( Real, StepInterval )
+    GET_METHOD( Real, StepInterval )
     {
         const Real aNextTime( getNextTime() );
         const Real aCurrentTime( getCurrentTime() );
@@ -157,10 +157,7 @@
         return aNextTime - aCurrentTime;
     }
 
-    SET_METHOD( Real, StepInterval )
-    {
-        setNextTime( getCurrentTime() + value );
-    }
+    virtual SET_METHOD( Real, StepInterval );
 
     /**
        This may be overridden in dynamically scheduled steppers.


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3854] ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp

[<mor...@us...>]

Revision: 3854
          http://ecell.svn.sourceforge.net/ecell/?rev=3854&view=rev
Author:   moriyoshi
Date:     2010-09-08 08:56:43 +0000 (Wed, 08 Sep 2010)

Log Message:
-----------
* Change Stepper wrapper so any non-predefined property can be assigned to.
* Throw AttributeError instead of RuntimeError when the property access fails.

Modified Paths:
--------------
    ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp

Modified: ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp
===================================================================
--- ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp	2010-08-30 11:46:06 UTC (rev 3853)
+++ ecell3/trunk/ecell/pyecell/ecell/_ecs.cpp	2010-09-08 08:56:43 UTC (rev 3854)
@@ -2688,7 +2688,9 @@
     return py::object( VariableReferences( self ) );
 }
 
-static Polymorph Entity___getattr__( Entity* self, std::string key )
+template< typename TecsObject_ >
+static Polymorph EcsObject___getattr__( TecsObject_* self, std::string key )
+try
 {
     if ( key == "__members__" || key == "__methods__" )
     {
@@ -2698,26 +2700,39 @@
 
     return self->getProperty( key );
 }
+catch ( NoSlot const& anException )
+{
+    PyErr_SetString( PyExc_AttributeError, anException.what() );
+    py::throw_error_already_set();
+    return Polymorph();
+}
 
-static void Entity___setattr__( py::object aSelf, py::object key, py::object value )
+template< typename TecsObject_ >
+static void EcsObject___setattr__( py::back_reference< TecsObject_* > aSelf, py::object key, py::object value )
+try
 {
-    py::handle<> aDescr( py::allow_null( PyObject_GetAttr( reinterpret_cast< PyObject* >( aSelf.ptr()->ob_type ), key.ptr() ) ) );
+    py::handle<> aDescr( py::allow_null( PyObject_GetAttr( reinterpret_cast< PyObject* >( aSelf.source().ptr()->ob_type ), key.ptr() ) ) );
     if ( !aDescr || !( aDescr->ob_type->tp_flags & Py_TPFLAGS_HAVE_CLASS ) || !aDescr.get()->ob_type->tp_descr_set )
     {
         PyErr_Clear();
-        Entity* self = py::extract< Entity* >( aSelf );
+        EcsObject* self = aSelf.get();
         std::string keyStr = py::extract< std::string >( key );
         self->setProperty( keyStr, py::extract< Polymorph >( value ) );
     }
     else
     {
-        aDescr.get()->ob_type->tp_descr_set( aDescr.get(), aSelf.ptr(), value.ptr() );
+        aDescr.get()->ob_type->tp_descr_set( aDescr.get(), aSelf.source().ptr(), value.ptr() );
         if (PyErr_Occurred())
         {
             py::throw_error_already_set();
         }
     }
 }
+catch ( NoSlot const& anException )
+{
+    PyErr_SetString( PyExc_AttributeError, anException.what() );
+    py::throw_error_already_set();
+}
 
 template< typename T_ >
 static PyObject* writeOnly( T_* )
@@ -2926,6 +2941,8 @@
                        &Stepper::getMinStepInterval,
                        &Stepper::setMinStepInterval )
         .add_property( "RngSeed", &writeOnly<Stepper>, &Stepper::setRngSeed )
+        .def( "__setattr__", &EcsObject___setattr__< Stepper > )
+        .def( "__getattr__", &EcsObject___getattr__< Stepper > )
         ;
 
     py::class_< Entity, py::bases<>, Entity, boost::noncopyable >
@@ -2937,8 +2954,8 @@
         .add_property( "ID", &Entity::getID, &Entity::setID )
         .add_property( "FullID", &Entity::getFullID )
         .add_property( "Name", &Entity::getName )
-        .def( "__setattr__", &Entity___setattr__ )
-        .def( "__getattr__", &Entity___getattr__ )
+        .def( "__setattr__", &EcsObject___setattr__< Entity > )
+        .def( "__getattr__", &EcsObject___getattr__< Entity > )
         ;
 
     py::class_< System, py::bases< Entity >, System, boost::noncopyable>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3853] ecell3/trunk/ecell/pyecell/ecell3-session.in

[<mor...@us...>]

Revision: 3853
          http://ecell.svn.sourceforge.net/ecell/?rev=3853&view=rev
Author:   moriyoshi
Date:     2010-08-30 11:46:06 +0000 (Mon, 30 Aug 2010)

Log Message:
-----------
* Do not implicitly chdir to the directory where the session script is placed.

Modified Paths:
--------------
    ecell3/trunk/ecell/pyecell/ecell3-session.in

Modified: ecell3/trunk/ecell/pyecell/ecell3-session.in
===================================================================
--- ecell3/trunk/ecell/pyecell/ecell3-session.in	2010-08-30 11:30:15 UTC (rev 3852)
+++ ecell3/trunk/ecell/pyecell/ecell3-session.in	2010-08-30 11:46:06 UTC (rev 3853)
@@ -49,11 +49,8 @@
 
     # Session methods
     def loadScript( self, ecs, parameters={} ):
-        ( ecsDir, ecsFile ) = os.path.split( ecs )
-        if ecsDir != '':
-            os.chdir( ecsDir )
         aContext = self.__createScriptContext( parameters )
-        execfile( ecsFile, aContext )
+        execfile( ecs, aContext )
 
     def interact( self, parameters = {} ):
         aContext = self.__createScriptContext( parameters )
@@ -83,6 +80,8 @@
 
 Options:
 
+    -C                                 :  change to the directory where
+                                          the script (.ess) file is placed.
     -e or --exec=[.ess file]           :  load script (.ess) file
     -f or --file=[.eml file]           :  load model (.eml) file
     
@@ -115,6 +114,7 @@
     # -------------------------------------
     anEmlFile = None
     anEssFile = None
+    chdirToEssFile = False
     anEmlFlag = 0
 
     aParameters = {}
@@ -139,7 +139,7 @@
     # -------------------------------------
     try:
         opts, args = getopt.gnu_getopt(
-            sys.argv[ 1: ] , 'he:f:D:',
+            sys.argv[ 1: ] , 'he:f:D:C',
             [ "parameters=", "help", "exec=", "file=" ] )
     except:
         usage()
@@ -171,6 +171,10 @@
                 sys.exit( -1 )
             anEmlFile = anArg            
 
+        # change directory where ESS file is placed.
+        if anOption == "-C":
+            chdirToEssFile = True
+
         # set session parameters            
         if anOption == "-D":
             aSplitArgList = anArg.split( '=' )
@@ -226,6 +230,9 @@
         aSession.loadModel( anEmlFile )
 
     if anEssFile:
+        if chdirToEssFile:
+            anEssDirectory, anEssFile = os.path.split( anEssFile )
+            os.chdir( anEssDirectory )
         aConsole.loadScript( anEssFile, aParameters )
     else:
         aConsole.interact( aParameters )


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3852] ecell3/trunk/ecell/pyecell/ecell/session_manager/ SessionManager.py

[<mor...@us...>]

Revision: 3852
          http://ecell.svn.sourceforge.net/ecell/?rev=3852&view=rev
Author:   moriyoshi
Date:     2010-08-30 11:30:15 +0000 (Mon, 30 Aug 2010)

Log Message:
-----------
Fix typo ;)

Modified Paths:
--------------
    ecell3/trunk/ecell/pyecell/ecell/session_manager/SessionManager.py

Modified: ecell3/trunk/ecell/pyecell/ecell/session_manager/SessionManager.py
===================================================================
--- ecell3/trunk/ecell/pyecell/ecell/session_manager/SessionManager.py	2010-08-16 05:32:34 UTC (rev 3851)
+++ ecell3/trunk/ecell/pyecell/ecell/session_manager/SessionManager.py	2010-08-30 11:30:15 UTC (rev 3852)
@@ -796,7 +796,7 @@
         return int : job id
         '''
         # creates AbstractSessionProxy
-        jva.suob = self.__theSystemProxy.createSessionProxy()
+        job = self.__theSystemProxy.createSessionProxy()
         job.setScriptFileName( scriptfile )
         job.setInterpreter( interpreter )
         if arguments != None:
@@ -853,7 +853,7 @@
         self.__theSystemProxy.getSessionProxy( jobid ).clear()
 
     def clearAllSessionProxies( self ):
-        for job in self.getSessionProxies():
+        for job in list(self.getSessionProxies()):
             job.clear()
 
     def clearRunningSessionProxies( self ):


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3851] ecell3/trunk/ecell/libecs/DifferentialStepper.cpp

[<mor...@us...>]

Revision: 3851
          http://ecell.svn.sourceforge.net/ecell/?rev=3851&view=rev
Author:   moriyoshi
Date:     2010-08-16 05:32:34 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
* DifferentialStepper::setStepInterval() isn't the same as Stepper::setStepInterval().

Modified Paths:
--------------
    ecell3/trunk/ecell/libecs/DifferentialStepper.cpp

Modified: ecell3/trunk/ecell/libecs/DifferentialStepper.cpp
===================================================================
--- ecell3/trunk/ecell/libecs/DifferentialStepper.cpp	2010-07-09 11:52:24 UTC (rev 3850)
+++ ecell3/trunk/ecell/libecs/DifferentialStepper.cpp	2010-08-16 05:32:34 UTC (rev 3851)
@@ -277,7 +277,7 @@
 
 void DifferentialStepper::updateInternalState( Real aStepInterval )
 {
-    setStepInterval( aStepInterval );
+    Stepper::setStepInterval( aStepInterval );
 
     // check if the step interval was changed, by epsilon
     if ( std::fabs( getTolerableStepInterval() - aStepInterval )


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3850] ecell3/trunk/NEWS

[<mor...@us...>]

Revision: 3850
          http://ecell.svn.sourceforge.net/ecell/?rev=3850&view=rev
Author:   moriyoshi
Date:     2010-07-09 11:52:24 +0000 (Fri, 09 Jul 2010)

Log Message:
-----------
* Update NEWS.

Modified Paths:
--------------
    ecell3/trunk/NEWS

Modified: ecell3/trunk/NEWS
===================================================================
--- ecell3/trunk/NEWS	2010-07-09 11:50:12 UTC (rev 3849)
+++ ecell3/trunk/NEWS	2010-07-09 11:52:24 UTC (rev 3850)
@@ -1,5 +1,7 @@
-ecell-3.2.1: 7-Jul-2010
+ecell-3.2.1: ?-Jul-2010
 
+ * Fix segmentation fault in PythonProcess and PythonFluxProcess.
+
  * Removed DifferentialStepper::initializeStepInterval() in favor of
    virtualized Stepper::setStepInterval().
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3849] ecell3/trunk/ecell/dm/PythonProcessBase.hpp

[<mor...@us...>]

Revision: 3849
          http://ecell.svn.sourceforge.net/ecell/?rev=3849&view=rev
Author:   moriyoshi
Date:     2010-07-09 11:50:12 +0000 (Fri, 09 Jul 2010)

Log Message:
-----------
* Fix segmentation fault

Modified Paths:
--------------
    ecell3/trunk/ecell/dm/PythonProcessBase.hpp

Modified: ecell3/trunk/ecell/dm/PythonProcessBase.hpp
===================================================================
--- ecell3/trunk/ecell/dm/PythonProcessBase.hpp	2010-07-09 11:49:40 UTC (rev 3848)
+++ ecell3/trunk/ecell/dm/PythonProcessBase.hpp	2010-07-09 11:50:12 UTC (rev 3849)
@@ -67,7 +67,7 @@
         }
     }
 
-    ~PythonProcessBase()
+    virtual ~PythonProcessBase()
     {
         // ; do nothing
     }
@@ -155,7 +155,7 @@
 
         // extract 'this' Process's methods and attributes
         boost::python::object aPySelfProcess(
-            boost::python::ptr( reinterpret_cast< libecs::Process* >( this ) ) );
+            boost::python::ptr( dynamic_cast< libecs::Process* const >( this ) ) );
 
         theGlobalNamespace[ "self" ] = aPySelfProcess;
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.