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.

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.