Updated "about" window. Displaying it at startup.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/Makefile
changed src/VirtualLeaf.cpp
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/canvas.h

Display the GPL license in a QMessageBox.

Enter commit message. Lines beginning with 'HG:' are removed.
Leave message empty to abort commit.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed doc/GPL
changed src/ChangeLog
changed src/canvas.cpp
changed src/canvas.h

Moved the Windows LIBXML2, LIBICONV and LIBZ libraries into the
destribtion, and changed the various project files accordingly.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added lib/libiconv/include/iconv.h
added lib/libiconv/include/libcharset.h
added lib/libiconv/include/localcharset.h
added lib/libiconv/lib/charset.alias
added lib/libiconv/lib/libcharset.la
added lib/libiconv/lib/libiconv.la
added lib/libiconv/share/doc/libiconv/COPYING
added lib/libiconv/share/doc/libiconv/COPYING.LIB
added lib/libiconv/share/doc/libiconv/NEWS
added lib/libiconv/share/doc/libiconv/NOTES
added lib/libxml2/include/libxml/DOCBparser.h
added lib/libxml2/include/libxml/HTMLparser.h
added lib/libxml2/include/libxml/HTMLtree.h
added lib/libxml2/include/libxml/SAX.h
added lib/libxml2/include/libxml/SAX2.h
added lib/libxml2/include/libxml/c14n.h
added lib/libxml2/include/libxml/catalog.h
added lib/libxml2/include/libxml/chvalid.h
added lib/libxml2/include/libxml/debugXML.h
added lib/libxml2/include/libxml/dict.h
added lib/libxml2/include/libxml/encoding.h
added lib/libxml2/include/libxml/entities.h
added lib/libxml2/include/libxml/globals.h
added lib/libxml2/include/libxml/hash.h
added lib/libxml2/include/libxml/list.h
added lib/libxml2/include/libxml/nanoftp.h
added lib/libxml2/include/libxml/nanohttp.h
added lib/libxml2/include/libxml/parser.h
added lib/libxml2/include/libxml/parserInternals.h
added lib/libxml2/include/libxml/pattern.h
added lib/libxml2/include/libxml/relaxng.h
added lib/libxml2/include/libxml/schemasInternals.h
added lib/libxml2/include/libxml/schematron.h
added lib/libxml2/include/libxml/threads.h
added lib/libxml2/include/libxml/tree.h
added lib/libxml2/include/libxml/uri.h
added lib/libxml2/include/libxml/valid.h
added lib/libxml2/include/libxml/xinclude.h
added lib/libxml2/include/libxml/xlink.h
added lib/libxml2/include/libxml/xmlIO.h
added lib/libxml2/include/libxml/xmlautomata.h
added lib/libxml2/include/libxml/xmlerror.h
added lib/libxml2/include/libxml/xmlexports.h
added lib/libxml2/include/libxml/xmlmemory.h
added lib/libxml2/include/libxml/xmlmodule.h
added lib/libxml2/include/libxml/xmlreader.h
added lib/libxml2/include/libxml/xmlregexp.h
added lib/libxml2/include/libxml/xmlsave.h
added lib/libxml2/include/libxml/xmlschemas.h
added lib/libxml2/include/libxml/xmlschemastypes.h
added lib/libxml2/include/libxml/xmlstring.h
added lib/libxml2/include/libxml/xmlunicode.h
added lib/libxml2/include/libxml/xmlversion.h
added lib/libxml2/include/libxml/xmlwin32version.h
added lib/libxml2/include/libxml/xmlwriter.h
added lib/libxml2/include/libxml/xpath.h
added lib/libxml2/include/libxml/xpathInternals.h
added lib/libxml2/include/libxml/xpointer.h
added lib/libxml2/lib/libxml2.dll
added lib/libxml2/lib/libxml2.lib
added lib/libz/include/zconf.h
added lib/libz/include/zlib.h
changed src/ChangeLog
changed src/Makefile
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/build_models/Makefile
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/libplugin.pro

Made additional formatting changes.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/VirtualLeaf.cpp
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.cpp
changed src/mesh.cpp
changed src/modelcatalogue.h
changed src/modelelement.h
changed src/node.cpp
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/xmlwrite.cpp

Removed any reference to perl from the project files.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/VirtualLeaf.pro
changed src/libplugin.pro

Reformatted the source files and generally straighten up the code.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/Neighbor.cpp
changed src/Neighbor.h
changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/UniqueMessage.h
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
changed src/build_models/translate_plugin.pl
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/cellitem.cpp
changed src/cellitem.h
changed src/curvecolors.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/far_mem_5.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.h
changed src/maxmin.h
changed src/mesh.cpp
changed src/mesh.h
changed src/miscq.cpp
changed src/miscq.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/modelelement.h
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeitem.h
changed src/nodeset.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/parse.cpp
changed src/parse.h
changed src/perl/deployapp.pl
changed src/perl/histogram.pl
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
changed src/perl/make_xmlwritecode.pl
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rseed.cpp
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
changed src/simplugin.cpp
changed src/simplugin.h
changed src/sqr.h
changed src/tiny.h
changed src/transporterdialog.cpp
changed src/transporterdialog.h
changed src/vector.cpp
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wall.h
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp
changed src/xmlwrite.h

Cleanup: e.g. removed commented out and otherwise disabled code.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parse.cpp
changed src/parse.h
changed src/random.cpp
changed src/random.h
changed src/sqr.h
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp

Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/VirtualLeaf.pro
changed src/xmlwrite.cpp
changed src/xmlwrite.h
removed src/xmlwritecode.cpp

Removed most compilation warnings; see ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed .hgignore
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/build_models/ChangeLog
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.cpp
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.h
changed src/forwardeuler.cpp
changed src/mainbase.h
changed src/mesh.cpp
changed src/nodeitem.cpp
changed src/output.cpp
changed src/qcanvasarrow.h
changed src/simitembase.cpp
changed src/xmlwrite.cpp

Wrapped diagnostic messages in QDEBUG blocks. Information messages still go to stderr.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/forwardeuler.cpp
changed src/mesh.cpp
changed src/mesh.h
changed src/random.cpp
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallitem.cpp

Issue #16: Removed leafplugin files; which leaves only auxingrowth, meinhardt and test plugins.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

removed src/build_models/leafplugin.cpp
removed src/build_models/leafplugin.h
removed src/build_models/plugin_leaf.pro

Added deployment code for MacOSX to VirtualLeaf.pro
Added MacOSX script for PackageMaker

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/vleafmacosx_installer.pmdoc/01virtualleaf-contents.xml
added src/vleafmacosx_installer.pmdoc/01virtualleaf.xml
added src/vleafmacosx_installer.pmdoc/02models-contents.xml
added src/vleafmacosx_installer.pmdoc/02models.xml
added src/vleafmacosx_installer.pmdoc/03leaves-contents.xml
added src/vleafmacosx_installer.pmdoc/03leaves.xml
added src/vleafmacosx_installer.pmdoc/index.xml
changed src/VirtualLeaf.pro

Added finalized tutorial code. Added new header files that provide simplified constructs for summing up concentrations in walls. Also added a new function for resetting all walls of a cell.
New menu items in canvas for resetting chemical values only in cells or only in walls.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial1A/mymodel.cpp
added src/TutorialCode/Tutorial1A/mymodel.h
added src/TutorialCode/Tutorial1A/mymodel.pro
added src/TutorialCode/Tutorial1B/mymodel.cpp
added src/TutorialCode/Tutorial1B/mymodel.h
added src/TutorialCode/Tutorial1B/mymodel.pro
added src/TutorialCode/Tutorial1C/mymodel.cpp
added src/TutorialCode/Tutorial1C/mymodel.h
added src/TutorialCode/Tutorial1C/mymodel.pro
added src/TutorialCode/Tutorial1D/mymodel.cpp
added src/TutorialCode/Tutorial1D/mymodel.h
added src/TutorialCode/Tutorial1D/mymodel.pro
added src/TutorialCode/Tutorial3/tutorial3_init.xml
added src/TutorialCode/Tutorial4/auxin_growth_init.xml
added src/TutorialCode/Tutorial4/mymodel
added src/TutorialCode/Tutorial4/tutorial4_init.xml
added src/TutorialCode/Tutorial5/mymodel
added src/TutorialCode/Tutorial5/tutorial5_init.xml
added src/flux_function.h
added src/vleafmodel.h
changed src/Makefile
changed src/TutorialCode/Tutorial2/mymodel.cpp
changed src/TutorialCode/Tutorial3/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.h
changed src/TutorialCode/Tutorial5/mymodel.cpp
changed src/TutorialCode/Tutorial5/mymodel.h
changed src/VirtualLeaf.pro
changed src/cellbase.cpp
changed src/cellbase.h

Removed from VirtualLeaf and libplugin project files their explicit perl invocation to regerenerate parameter files.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/Makefile
changed src/VirtualLeaf.pro
changed src/build_models/Makefile
changed src/libplugin.pro

Added to new menu options: edit->ResetChemicals and edit->ResetTransporters, which allows you to set only the chemicals or only the transporters to the initial values. I needed this for preparing a suitable initial condition for Tutorial 6 and thought it would be useful for the main distribution.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h

Updated the Makefiles and updated testplugin to new plugin interface.

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/Makefile
added src/build_models/Makefile
changed src/VirtualLeaf.pro
changed src/build_models/leafplugin.cpp
changed src/build_models/leafplugin.h
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
removed src/build_models/simplugin.h

Tweaked project files to delete/regenerate parameter and pardialog files only if perl is installed. Added new top-level Makefiles. See ChangeLogs for more details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added src/Makefile
added src/build_models/Makefile
added src/parameter.cpp
added src/parameter.h
added src/pardialog.cpp
added src/pardialog.h
changed .hgignore
changed src/ChangeLog
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/libplugin.pro

Changed interface for model plugins to make usage of pointers and references consistent.
Added codes for tutorial belonging to VLeaf manuscript.
Something changed in modelcatalogue. I'm not sure what...

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial0/mymodel.cpp
added src/TutorialCode/Tutorial0/mymodel.h
added src/TutorialCode/Tutorial0/mymodel.pro
added src/TutorialCode/Tutorial1/mymodel.cpp
added src/TutorialCode/Tutorial1/mymodel.h
added src/TutorialCode/Tutorial1/mymodel.pro
added src/TutorialCode/Tutorial2/mymodel.cpp
added src/TutorialCode/Tutorial2/mymodel.h
added src/TutorialCode/Tutorial2/mymodel.pro
added src/TutorialCode/Tutorial3/mymodel.cpp
added src/TutorialCode/Tutorial3/mymodel.h
added src/TutorialCode/Tutorial3/mymodel.pro
added src/TutorialCode/Tutorial4/mymodel.cpp
added src/TutorialCode/Tutorial4/mymodel.h
added src/TutorialCode/Tutorial4/mymodel.pro
added src/TutorialCode/Tutorial5/mymodel.cpp
added src/TutorialCode/Tutorial5/mymodel.h
added src/TutorialCode/Tutorial5/mymodel.pro
added src/build_models/translate_plugin.pl
changed src/VirtualLeafpar.tmpl
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h

Roeland's recent improvements - especially a more robust Mesh::Derivatives().

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/mesh.cpp
changed src/mesh.h

Oh, oh... my previous solution to clean and then reconstruct a new initial condition did not work in all cases. Now I am calling Init(leaffile) during startup initialization only if the user is passing a leafML file during startup (-l option).

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.cpp
changed src/modelcatalogue.cpp

I have replaced the instances of strtod for the Qt conversion functions via QLocale. Possibly there is some remaining usage of atof and atoi.

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/perl/make_parameter_source.pl
changed src/xmlwrite.cpp

Corrected problem with "testmodel": the standard initial condition (a polygon) was no longer constructed.

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/modelcatalogue.cpp

I've repaired VLeaf's batch mode to work with dynamic model loading. There is a new option now "-m" that allows you to supply a model name.

For example:

./VirtualLeaf -l ../data/leaves/auxin_growth.xml -m libauxingrowth.so -b

or

./VirtualLeaf --leaffile ../data/leaves/auxin_growth.xml --model libauxingrowth.so --batch


user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/warning.cpp

Look at the libraries and paths in win32:LIB in VirtualLeaf.pro.
The libraries libxml2 and libiconv are individually installed in C:,
and libiconv.dll.a copied, i.e. renamed, to libiconv.a.
At least everything compiles and links.