2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and

	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with

	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with

	mesh.incrementIterations().

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Turned debug off to make all profiles must be

	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX

	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the

	uninstaller all go in the bin directory. And leaves directory

	placed under data directory.

	* canvas.cpp (exportCellData): Added a check to inquire before

	overwritting an existing file.

2010-10-14    <merks@cwi.nl>

	* mesh.cpp: In response to referees' comments, added new parameter

	"yield_threshold" instead of fixed parameter '4' for yield

	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was

	cycled and the transporterdialog popped up. Corrected this - for

	wall type cycling, hold the Control button while left

	clicking. TransporterDialog only pops up for left click. Also made

	sure the wall is redrawn after changing the transporter values.

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

	* cellbase.cpp (ExactCircumference): I added a new function

	ExactCircumference, yielding the circumference of the cell along

	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates

	need to be sorted in x,y order for the convex hull algorithm

	(thanks Margriet!). I updated CSVExportCellData so it exports the

	circumferences of hull and boundary_polygon.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:

	(TimeStamp): New private TimeStamp() function.

	(TimeStepWrap): Added invocation of exportCellData().

	(exportCellData): Created two polymorphic functions: one with a

	single QString argument, the other with no argument. The former is

	called from TimeStepWrap() while the latter is called from the

	"Export cell areas" item in the file menu.

2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire

	where to write the exportCellData.

2010-06-28    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc

	directory (Linux) or a decedent doc directory (Windows, via the

	binary installer).

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.

	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.

	Add missing libiconv/bin, libxml2bin and libz/bin directories.

	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

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

	* libplugin.pro: Use correct library path.

	* VirtualLeaf.pro: Ditto.

	* 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.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: VirtualLeaf libplugin plugins tutorials

VirtualLeaf: Makefile.VirtualLeaf

	$(MAKE) -f Makefile.VirtualLeaf

Makefile.VirtualLeaf: VirtualLeaf.pro

libplugin: Makefile.libplugin

	$(MAKE) -f Makefile.libplugin

Makefile.libplugin: libplugin.pro

plugins:

	$(MAKE) -C build_models -f Makefile

tutorials:

	$(MAKE) -C build_models -f Makefile

	$(MAKE) -C TutorialCode -f Makefile

clean:

	$(MAKE) -f Makefile.libplugin clean

	$(MAKE) -f Makefile.VirtualLeaf clean

	$(MAKE) -C build_models -f Makefile clean

	$(MAKE) -C TutorialCode -f Makefile clean

ifeq ($(MAKE),make)

	touch VirtualLeaf.pro

	touch libplugin.pro

else

	copy /b VirtualLeaf.pro +,,

	copy /b libplugin.pro +,,

endif

#finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial0.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial0.pro: Corrected windows library paths.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial0

tutorial0: Makefile.tutorial0

	$(MAKE) -f Makefile.tutorial0

Makefile.tutorial0: tutorial0.pro

clean:

	$(MAKE) -f Makefile.tutorial0 clean

ifeq ($(MAKE),make)

	touch tutorial0.pro

else

	copy /b tutorial0.pro +,,

endif

# finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial1A.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial1A.pro: corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial1A

tutorial1A: Makefile.tutorial1A

	$(MAKE) -f Makefile.tutorial1A

Makefile.tutorial1A: tutorial1A.pro

clean:

	$(MAKE) -f Makefile.tutorial1A clean

ifeq ($(MAKE),make)

	touch tutorial1A.pro

else

	copy /b tutorial1A.pro +,,

endif

# finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial1B.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial1B.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make. 

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial1B

tutorial1B: Makefile.tutorial1B

	$(MAKE) -f Makefile.tutorial1B

Makefile.tutorial1B: tutorial1B.pro

clean:

	$(MAKE) -f Makefile.tutorial1B clean

ifeq ($(MAKE),make)

	touch tutorial1B.pro

else

	copy /b tutorial1B.pro +,,

endif

# finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial1C.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial1C.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial1C

tutorial1C: Makefile.tutorial1C

	$(MAKE) -f Makefile.tutorial1C

Makefile.tutorial1C: tutorial1C.pro

clean:

	$(MAKE) -f Makefile.tutorial1C clean

ifeq ($(MAKE),make)

	touch tutorial1C.pro

else

	copy /b tutorial1C.pro +,,

endif

# finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial1D.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial1D.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial1D

tutorial1D: Makefile.tutorial1D

	$(MAKE) -f Makefile.tutorial1D

Makefile.tutorial1D: tutorial1D.pro

clean:

	$(MAKE) -f Makefile.tutorial1D clean

ifeq ($(MAKE),make)

	touch tutorial1D.pro

else

	copy /b tutorial1D.pro +,,

endif

# finis

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial2.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial2.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial2

tutorial2: Makefile.tutorial2

	$(MAKE) -f Makefile.tutorial2

Makefile.tutorial2: tutorial2.pro

clean:

	$(MAKE) -f Makefile.tutorial2 clean

ifeq ($(MAKE),make)

	touch tutorial2.pro

else

	copy /b tutorial2.pro +,,

endif

# finis

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.h (SimPluginInterface): Added default LeafML file.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial3.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial3

tutorial3: Makefile.tutorial3

	$(MAKE) -f Makefile.tutorial3

Makefile.tutorial3: tutorial3.pro

clean:

	$(MAKE) -f Makefile.tutorial3 clean

ifeq ($(MAKE),make)

	touch tutorial3.pro

else

	copy /b tutorial3.pro +,,

endif

# finis

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* tutorial4.h (SimPluginInterface): Added default LeafML file.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial4.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial4.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial4

tutorial4: Makefile.tutorial4

	$(MAKE) -f Makefile.tutorial4

Makefile.tutorial4: tutorial4.pro

clean:

	$(MAKE) -f Makefile.tutorial4 clean

ifeq ($(MAKE),make)

	touch tutorial4.pro

else

	copy /b tutorial4.pro +,,

endif

# finis

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* tutorial5.h (SimPluginInterface): Added default LeafML file.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial5.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

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

	* tutorial5.pro: Corrected windows library path.

# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: tutorial5

tutorial5: Makefile.tutorial5

	$(MAKE) -f Makefile.tutorial5

Makefile.tutorial5: tutorial5.pro

clean:

	$(MAKE) -f Makefile.tutorial5 clean

ifeq ($(MAKE), make)

	touch tutorial5.pro

else

	copy /b tutorial5.pro +,,

endif

# finis

#  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 += -Wno-write-strings

QMAKE_CXXFLAGS += -Wno-unused-parameter

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

LIBDIR = ../lib

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

 LIBXML2DIR = $${LIBDIR}\libxml2

 LIBICONVDIR = $${LIBDIR}\libiconv

 LIBZDIR = $${LIBDIR}\libz

 GRAPHICS = qt 

 RC_FILE = VirtualLeaf.rc

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 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 \

       hull.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 \