Corrected some problems with software deployment on MacOSX.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added doc/mac-deploy-howto.txt
added src/perl/deploymodel.pl
changed src/VirtualLeaf.pro

In response to referee's comment:

"I am also afraid that

the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very
well in my hands, could the program be changed so that the correct file
extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically."

I corrected the "export cell data" dialog (it did not actually write the file in the submitted version). Also we now assume default file extensions (.jpg for snapshot and .csv for data export) if none is given.

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

Removed erroneous qmake -makefile option. MACOSX, look for gpl3.txt in ../doc directory.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/Makefile
changed src/TutorialCode/Tutorial0/ChangeLog
changed src/TutorialCode/Tutorial0/Makefile
changed src/TutorialCode/Tutorial1A/ChangeLog
changed src/TutorialCode/Tutorial1A/Makefile
changed src/TutorialCode/Tutorial1B/ChangeLog
changed src/TutorialCode/Tutorial1B/Makefile
changed src/TutorialCode/Tutorial1C/ChangeLog
changed src/TutorialCode/Tutorial1C/Makefile
changed src/TutorialCode/Tutorial1D/ChangeLog
changed src/TutorialCode/Tutorial1D/Makefile
changed src/TutorialCode/Tutorial2/ChangeLog
changed src/TutorialCode/Tutorial2/Makefile
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/Makefile
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/Makefile
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/Makefile
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/build_models/Makefile

Tweaked Windows installation directories. Turned debugging off in
VirtualLeaf profile - all profiles must be consistent.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/VirtualLeaf-install.nsi
changed src/VirtualLeaf.pro

Made changes to conform to the version submitted with the Plant Physiology paper. See the individual ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added lib/libiconv/bin/iconv.exe
added lib/libiconv/bin/libcharset-1.dll
added lib/libiconv/bin/libiconv-2.dll
added src/gpl3.txt
changed INSTALL
changed src/ChangeLog
changed src/TutorialCode/Tutorial0/ChangeLog
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/TutorialCode/Tutorial1A/ChangeLog
changed src/TutorialCode/Tutorial1A/tutorial1A.pro
changed src/TutorialCode/Tutorial1B/ChangeLog
changed src/TutorialCode/Tutorial1B/tutorial1B.pro
changed src/TutorialCode/Tutorial1C/ChangeLog
changed src/TutorialCode/Tutorial1C/tutorial1C.pro
changed src/TutorialCode/Tutorial1D/ChangeLog
changed src/TutorialCode/Tutorial1D/tutorial1D.pro
changed src/TutorialCode/Tutorial2/ChangeLog
changed src/TutorialCode/Tutorial2/tutorial2.pro
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3.pro
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/tutorial4.pro
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/tutorial5.pro
changed src/VirtualLeaf-install.nsi
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/canvas.cpp
changed src/libplugin.pro
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
removed doc/gpl3.txt

Use Correct library path in various project files.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
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

In DrawCell class (VirtualLeaf.cpp) - iterate over NChem to construct info_string. Additional cleanup.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
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/VirtualLeaf.pro
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
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/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/libplugin.pro
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.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/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/parse.cpp
changed src/parse.h
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
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/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

* Added functionality for numerical output (CSV) format. See functions starting with "CSV" in mesh.cpp. External code hull.cpp is responsible for convex hull calculations.
- ToDo: adopt menu item "File->export cell areas" so user can choose a file name or set up periodic output of numerical data.
- ToDo: add parameters re: periodic numeric output to "<settings>" block of LeafML-file, so it becomes possible to set up numeric output interactively, then write the LeafML file and run the program in batch mode to retrieve periodic numeric output.

* Added new functionality to plugin interface. It becomes possible to define a default LeafML init file for a plugin. It is read whenever the model plugin is loaded.
- ToDo: define default LeafML files for all plugins, according to the LeafML files mentioned in the Plant Phys. tutorial.


user: Roeland Merks <merks@cwi.nl>
branch 'default'
added src/hull.cpp
added src/hull.h
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.cpp
changed src/simplugin.h
changed src/xmlwrite.cpp

Cleaned up leaves directory. Disabled console mode, Updated nsi script.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added data/leaves/ChangeLog
added data/leaves/tutorial3_init.xml
added data/leaves/tutorial4_init.xml
added data/leaves/tutorial5_init.xml
changed data/leaves/auxin.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed data/leaves/schemas.xml
changed data/leaves/vleaf.rnc
changed data/leaves/vleaf.rng
changed data/leaves/vleaf.xml
changed data/leaves/vleaf.xsd
changed data/leaves/vleaf2.xml
changed doc/installation.pdf
changed doc/installation.rst
changed src/ChangeLog
changed src/VirtualLeaf-install.nsi
changed src/VirtualLeaf.pro
removed data/leaves/bend.xml
removed data/leaves/circ.xml
removed data/leaves/explant.xml
removed data/leaves/init.xml
removed data/leaves/one_acc_point_van3.xml
removed data/leaves/one_acc_point_van3_growth.xml
removed data/leaves/one_acc_point_van3_growth2.xml
removed data/leaves/tissue.xml

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

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

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

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

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

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

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.