2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* simitembase.cpp: Removed NULL assignments to unused variables.

	* VirtualLeaf.cpp: Ditto.

	* apoplastitem.cpp: Ditto.

	* canvas.cpp: Ditto.

	* cell.cpp: Ditto.

	* cellbase.h: Ditto.

	* forwardeuler.cpp: Ditto.

	* mainbase.h: Ditto.

	* nodeitem.cpp: Ditto.

	* qcanvasarrow.h: Ditto.

	* simitembase.cpp: Ditto.

	* Makefile (clean): Add -f Makefile argument to each make invocation.

	* VirtualLeaf-install.nsi: New gpl license text.

	* VirtualLeaf.pro: Disabled console mode.

	* mesh.cpp (Clear): Added parentheses to qDebug statments.

	(TestIllegalWalls): Replaced qDebug().

	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.

	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* parameter.cpp: Added particular reassignment of datadir.

	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (gpl): Added gpl slot to display GPL license.

	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.

	* libplugin.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.

	* libplugin.pro: Ditto.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.

	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.

	* xmlwrite.h (XMLIO): Ditto!

	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;

	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur

	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.

	(XMLReadCells): Removed unused count variable.

	(XMLReadSimtime): Removed unused cur variable.

	(XMLRead): Removed unused v_str variable.

	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.

	(SimItemBase) Ditto.

	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.

	* output.cpp (OpenWriteFile): Removed unused par variable.

	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.

	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.

	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.

	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.

	(mousePressEvent): Removed unused item variable.

	* apoplastitem.cpp

	(ApoplastItem): Removed unused par variable.

	(OnClick): Use NULL assignment merely to obviate compilation warning.

	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.

	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.

	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.

	* VirtualLeaf.cpp ditto.

	* canvas.cpp ditto.

	* cell.cpp ditto.

	* data_plot.cpp ditto.

	* forwardeuler.cpp ditto.

	* mesh.cpp ditto.

	* mesh.h

	* random.cpp ditto.

	* wall.cpp ditto.

	* wallbase.cpp ditto.

	* wallitem.cpp ditto.

2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.

	* libplugin.pro: ditto.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h: Added default versions of this automatically generated file.

	* pardialog.cpp: ditto.

	* parameter.h: ditto.

	* parameter.cpp: ditto.

	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.

 	* libplugin.pro: dito.

	* Makefile: Added top-level Makefile

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

#

#  $Id$

#

#  This file is part of the Virtual Leaf.

#

#  The Virtual Leaf is free software: you can redistribute it and/or modify

#  it under the terms of the GNU General Public License as published by

#  the Free Software Foundation, either version 3 of the License, or

#  (at your option) any later version.

#

#  The Virtual Leaf is distributed in the hope that it will be useful,

#  but WITHOUT ANY WARRANTY; without even the implied warranty of

#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#  GNU General Public License for more details.

#

#  You should have received a copy of the GNU General Public License

#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

#

#  Copyright 2010 Roeland Merks.

#

CONFIG += release

CONFIG -= debug

CONFIG += qt

QMAKE_CXXFLAGS += -fexceptions

QMAKE_CXXFLAGS += -Wall

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

#REACTIONS = reactions_auxin_growth.h 

#REACTIONS = reactions_meinhardt.h

#REACTIONS = reactions_pce_growth.h

DEFINES += QTGRAPHICS

DEFINES += REACTIONS_HEADER=$${REACTIONS}

DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"

DEFINES += FLEMING

BINDIR = ../bin

DESTDIR = $$BINDIR

TARGET = VirtualLeaf

TEMPLATE = app

PARTMPL = $${TARGET}par.tmpl

MAINSRC = $${TARGET}.cpp

QT -= network sql xml

QT += qt3support

!win32 {

 GRAPHICS = qt #qwt

}

win32 {

 CONFIG -= console

 GRAPHICS = qt 

 RC_FILE = VirtualLeaf.rc

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

 LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv

}

macx:release {

 LIBS+= -dead_strip

}

unix {

 CC = /usr/bin/gcc 

 QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn

 QMAKE_LIBDIR += $$QWTDIR/lib 

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

 LIBS += -lxml2 -lz -lm 

}

# Input

HEADERS += \

# apoplastitem.h \

 canvas.h \

 cellbase.h \

 cell.h \

 cellitem.h \

 forwardeuler.h \

 infobar.h \

 mainbase.h \

 mainbase.h \

 matrix.h \

 mesh.h \

 miscq.h \

 modelcatalogue.h \

 Neighbor.h \

 node.h \

 nodeitem.h \

 nodeset.h \

 OptionFileDialog.h \

 output.h \

 parameter.h \

 pardialog.h \

 parse.h \

 pi.h \

 qcanvasarrow.h \

 random.h \

 rungekutta.h \

 simitembase.h \

 simplugin.h \

 sqr.h \

 tiny.h \

 transporterdialog.h \

 UniqueMessage.h \

 vector.h \

 wallbase.h \

 wall.h \

 wallitem.h \

 warning.h \

 xmlwrite.h \

 $${PARTMPL}

SOURCES += \

# apoplastitem.cpp \

 canvas.cpp \

 cellbase.cpp \

 cell.cpp \

 cellitem.cpp \

 forwardeuler.cpp \

 mainbase.cpp \

 matrix.cpp \

 mesh.cpp \

 miscq.cpp \

 modelcatalogue.cpp \

 Neighbor.cpp \

 node.cpp \

 nodeitem.cpp \

 nodeset.cpp \

 OptionFileDialog.cpp \

 output.cpp \

 parameter.cpp \

 pardialog.cpp \

 parse.cpp \

 random.cpp \

 rungekutta.cpp \

 simitembase.cpp \

 transporterdialog.cpp \

 UniqueMessage.cpp \

 vector.cpp \

 wallbase.cpp \

 wall.cpp \

 wallitem.cpp \

 warning.cpp \

 xmlwrite.cpp \

 $$MAINSRC

contains( TARGET, leaf_fleming ) {

 DEFINES += FLEMING	

}

contains(GRAPHICS, qwt) {

 #macx:LIBS += -L$$QWTDIR/lib -lqwt

 #win32:LIBS += -L$$QWTDIR/lib -lqwt5

 #LIBS += -L$$QWTDIR/lib -lqwt

 INCLUDEPATH += $$QWTDIR/include

 DEFINES += HAVE_QWT

 HEADERS += data_plot.h

 SOURCES += data_plot.cpp

}

contains( GRAPHICS, qt ) {

 message( "Building Qt executable" )

 QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive

}

contains( GRAPHICS, xfig ) {

 message("Building Xfig executable (background runnable).")

 QMAKE_CXXFLAGS += -DXFIGGRAPHICS

}

contains( GRAPHICS, x11 ) {

 !unix {

  error("X11 graphics only available on Unix systems.")

 }

 message("Building X11 executable")

 SOURCES += x11graph.cpp

 HEADERS += x11graph.h

 QMAKE_CXXFLAGS += -DX11GRAPHICS

 CONFIG -= qt

 CONFIG += x11

 unix:LIBS += -lpng

}

#contains( GRAPHICS, qwt ) {

# 	QMAKE_POST_LINK = "install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \

#}

# MACOSX packaging

macx {

ICON = leaficon.icns

QMAKE_POST_LINK = "\

	#install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \

	cp leaficon.icns $${DESTDIR}/$${TARGET}.app; \

	mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

	cp -R /Library/Frameworks/QtCore.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

	cp -R /Library/Frameworks/QtGui.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

	cp -R /Library/Frameworks/Qt3Support.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

	#cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

	#install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \

	install_name_tool -change /usr/local/qwt/lib/libqwt.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\

	install_name_tool -id @executable_path/../Frameworks/QtCore.framework/Versions/Current/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtCore.framework/Versions/4.0/QtCore; \

	install_name_tool -id @executable_path/../Frameworks/QtGui.framework/Versions/Current/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui; \

	install_name_tool -id @executable_path/../Frameworks/Qt3Support.framework/Versions/Current/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \

	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \

	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \

	install_name_tool -change Frameworks/Qt3Support.framework/Versions/Current/Qt3Support @executable_path/../Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \

	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \

	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \

	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; "

}

# finis

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* auxingrowthplugin.cpp: Removed NULL assignments to unused variables.

	* meinhardtplugin.cpp: Ditto.

	* testplugin.cpp: Ditto.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (clean): Add windows equivalent of UNIX touch.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* plugin_auxingrowth.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.

	* plugin_meinhardt.pro: Ditto.

	* plugin_test.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* testplugin.cpp (CelltoCellTransport) Use NULL assignment merely to obviate compilation warnings.

	(WallDynamics): Ditto.

	(CellDynamics): Ditto.

	(OnDivide): Ditto.

	* meinhardtplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.

	* (WallDynamics): Ditto.

	* auxingrowthplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* Makefile: Added top-level Makefile.

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* plugin_test.pro: Added -fPIC option to QMAKE_CXXFLAGS.

	* plugin_meinhardt.pro: ditto

	* plugin_auxingrowth.pro: ditto

#

# $Id$

#

#  This file is part of the Virtual Leaf.

#

#  The Virtual Leaf is free software: you can redistribute it and/or modify

#  it under the terms of the GNU General Public License as published by

#  the Free Software Foundation, either version 3 of the License, or

#  (at your option) any later version.

#

#  The Virtual Leaf is distributed in the hope that it will be useful,

#  but WITHOUT ANY WARRANTY; without even the implied warranty of

#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#  GNU General Public License for more details.

#

#  You should have received a copy of the GNU General Public License

#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

#

#  Copyright 2010 Roeland Merks.

#

CONFIG += release

CONFIG -= debug

CONFIG += plugin

BINDIR = ../../bin

LIBDIR = ../../lib

DEFINES = QTGRAPHICS # VLEAFPLUGIN

DESTDIR = $${BINDIR}/models

TARGET = auxingrowth

HEADERS = ../simplugin.h $${TARGET}plugin.h  

QMAKE_CXXFLAGS += -fexceptions -I..

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QT += qt3support

SOURCES = $${TARGET}plugin.cpp

TEMPLATE = lib 

unix {

 LIBS += -L$${LIBDIR} -lvleaf

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

# finis

#

# $Id$

#

#  This file is part of the Virtual Leaf.

#

#  The Virtual Leaf is free software: you can redistribute it and/or modify

#  it under the terms of the GNU General Public License as published by

#  the Free Software Foundation, either version 3 of the License, or

#  (at your option) any later version.

#

#  The Virtual Leaf is distributed in the hope that it will be useful,

#  but WITHOUT ANY WARRANTY; without even the implied warranty of

#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#  GNU General Public License for more details.

#

#  You should have received a copy of the GNU General Public License

#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

#

#  Copyright 2010 Roeland Merks.

#

CONFIG += release

CONFIG -= debug

CONFIG += plugin

BINDIR = ../../bin

LIBDIR = ../../lib

DEFINES = QTGRAPHICS # VLEAFPLUGIN

DESTDIR = $${BINDIR}/models

TARGET = meinhardt

HEADERS = ../simplugin.h $${TARGET}plugin.h  

QMAKE_CXXFLAGS += -fexceptions -I..

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QT += qt3support

SOURCES = $${TARGET}plugin.cpp

TEMPLATE = lib 

unix {

 LIBS += -L$${LIBDIR} -lvleaf

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

# finis

#

# $Id$

#

#  This file is part of the Virtual Leaf.

#

#  The Virtual Leaf is free software: you can redistribute it and/or modify

#  it under the terms of the GNU General Public License as published by

#  the Free Software Foundation, either version 3 of the License, or

#  (at your option) any later version.

#

#  The Virtual Leaf is distributed in the hope that it will be useful,

#  but WITHOUT ANY WARRANTY; without even the implied warranty of

#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#  GNU General Public License for more details.

#

#  You should have received a copy of the GNU General Public License

#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

#

#  Copyright 2010 Roeland Merks.

#

CONFIG += release

CONFIG -= debug

CONFIG += plugin

BINDIR = ../../bin

LIBDIR = ../../lib

DEFINES = QTGRAPHICS # VLEAFPLUGIN

DESTDIR = $${BINDIR}/models

TARGET = test

HEADERS = ../simplugin.h $${TARGET}plugin.h  

QMAKE_CXXFLAGS += -fexceptions -I..

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QT += qt3support

SOURCES = $${TARGET}plugin.cpp

TEMPLATE = lib 

unix {

 LIBS += -L$${LIBDIR} -lvleaf

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

# finis

#

#  $Id$

#

#  This file is part of the Virtual Leaf.

#

#  The Virtual Leaf is free software: you can redistribute it and/or modify

#  it under the terms of the GNU General Public License as published by

#  the Free Software Foundation, either version 3 of the License, or

#  (at your option) any later version.

#

#  The Virtual Leaf is distributed in the hope that it will be useful,

#  but WITHOUT ANY WARRANTY; without even the implied warranty of

#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#  GNU General Public License for more details.

#

#  You should have received a copy of the GNU General Public License

#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

#

#  Copyright 2010 Roeland Merks.

#

CONFIG += release

CONFIG -= debug

CONFIG += staticlib

QMAKE_CXXFLAGS += -fexceptions

win32:QMAKE_CXXFLAGS -= O2

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions

DEFINES = QTGRAPHICS # VLEAFPLUGIN

DESTDIR = ../lib 

PARTMPL = VirtualLeafpar.tmpl

QT += qt3support

TARGET = vleaf

TEMPLATE = lib

HEADERS = \

 cellbase.h \

 matrix.h \

 output.h \

 parameter.h \

 parse.h \

 random.h \

 simplugin.h \

 UniqueMessage.h \

 vector.h \

 wallbase.h \

 warning.h

SOURCES = \

 cellbase.cpp \

 matrix.cpp \

 output.cpp \

 parameter.cpp \

 parse.cpp \

 random.cpp \

 simplugin.cpp \

 UniqueMessage.cpp \

 vector.cpp \

 wallbase.cpp \

 warning.cpp

unix {

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

 LIBS += -lxml2 -lz -lm 

}

win32 {

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

#