Some last fine-tuning
- File dialogs start from appropriate data directories
- XML files contain right values for datadir
- Reordered parameter dialog
- Added new "make perl" heading to the makefile
- Corrected segfault for batch mode

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
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changed src/Makefile
changed src/VirtualLeaf.cpp
changed src/VirtualLeafpar.tmpl
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changed src/pardialog.cpp
changed src/pardialog.h

A few last updates before submitting the revised Plant Phys. paper. Corrected the invocation of TransporterDialog and added parameter 'yield_threshold'

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/VirtualLeafpar.tmpl
changed src/mesh.cpp
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changed src/pardialog.h
changed src/wallitem.cpp

Use iteration number instead of time stamp to tag exported cell data files. Added default LeafML files to tutorials 3-5. See respective ChangeLogs for details.

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user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
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Export Cell Data at interval specified in the leafML file or explicitly via the file menu.
Added new parameters to VirtualLeafpar.tmpl
Added GPL boilerplate to make_{parameter,pardialog}_source.pl files.
Added new parameters to auxin_growth.xml. See respective ChangeLog files for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed src/ChangeLog
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
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changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl

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
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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
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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
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changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/node.cpp
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changed src/nodeset.cpp
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changed src/output.cpp
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changed src/pi.h
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changed src/random.cpp
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changed src/rungekutta.cpp
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changed src/simitembase.cpp
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changed src/transporterdialog.cpp
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changed src/warning.cpp
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changed src/xmlwrite.cpp
changed src/xmlwrite.h

Renamed tutorial examples and added makefile, etc.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added doc/gpl3.txt
added doc/installation.pdf
added doc/installation.rst
added src/TutorialCode/Makefile
added src/TutorialCode/Tutorial0/Makefile
added src/TutorialCode/Tutorial0/tutorial0.cpp
added src/TutorialCode/Tutorial0/tutorial0.h
added src/TutorialCode/Tutorial0/tutorial0.pro
added src/TutorialCode/Tutorial1A/Makefile
added src/TutorialCode/Tutorial1A/tutorial1A.cpp
added src/TutorialCode/Tutorial1A/tutorial1A.h
added src/TutorialCode/Tutorial1A/tutorial1A.pro
added src/TutorialCode/Tutorial1B/Makefile
added src/TutorialCode/Tutorial1B/tutorial1B.cpp
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added src/TutorialCode/Tutorial1C/Makefile
added src/TutorialCode/Tutorial1C/tutorial1C.cpp
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added src/TutorialCode/Tutorial1D/Makefile
added src/TutorialCode/Tutorial1D/tutorial1D.cpp
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added src/TutorialCode/Tutorial2/Makefile
added src/TutorialCode/Tutorial2/tutorial2.cpp
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added src/TutorialCode/Tutorial2/tutorial2.pro
added src/TutorialCode/Tutorial3/Makefile
added src/TutorialCode/Tutorial3/tutorial3.cpp
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added src/TutorialCode/Tutorial4/Makefile
added src/TutorialCode/Tutorial4/tutorial4.cpp
added src/TutorialCode/Tutorial4/tutorial4.h
added src/TutorialCode/Tutorial4/tutorial4.pro
added src/TutorialCode/Tutorial5/Makefile
added src/TutorialCode/Tutorial5/tutorial5.cpp
added src/TutorialCode/Tutorial5/tutorial5.h
added src/TutorialCode/Tutorial5/tutorial5.pro
added src/perl/ChangeLog
changed src/ChangeLog
changed src/Makefile
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changed src/canvas.cpp
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changed src/parameter.h
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changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
changed src/perl/make_xmlwritecode.pl
changed src/vleafmodel.h
removed doc/GPL
removed src/TutorialCode/Tutorial0/mymodel.cpp
removed src/TutorialCode/Tutorial0/mymodel.h
removed src/TutorialCode/Tutorial0/mymodel.pro
removed src/TutorialCode/Tutorial1/mymodel.cpp
removed src/TutorialCode/Tutorial1/mymodel.h
removed src/TutorialCode/Tutorial1/mymodel.pro
removed src/TutorialCode/Tutorial1A/mymodel.cpp
removed src/TutorialCode/Tutorial1A/mymodel.h
removed src/TutorialCode/Tutorial1A/mymodel.pro
removed src/TutorialCode/Tutorial1B/mymodel.cpp
removed src/TutorialCode/Tutorial1B/mymodel.h
removed src/TutorialCode/Tutorial1B/mymodel.pro
removed src/TutorialCode/Tutorial1C/mymodel.cpp
removed src/TutorialCode/Tutorial1C/mymodel.h
removed src/TutorialCode/Tutorial1C/mymodel.pro
removed src/TutorialCode/Tutorial1D/mymodel.cpp
removed src/TutorialCode/Tutorial1D/mymodel.h
removed src/TutorialCode/Tutorial1D/mymodel.pro
removed src/TutorialCode/Tutorial2/mymodel.cpp
removed src/TutorialCode/Tutorial2/mymodel.h
removed src/TutorialCode/Tutorial2/mymodel.pro
removed src/TutorialCode/Tutorial3/mymodel.cpp
removed src/TutorialCode/Tutorial3/mymodel.h
removed src/TutorialCode/Tutorial3/mymodel.pro
removed src/TutorialCode/Tutorial4/mymodel
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removed src/TutorialCode/Tutorial4/mymodel.h
removed src/TutorialCode/Tutorial4/mymodel.pro
removed src/TutorialCode/Tutorial5/mymodel
removed src/TutorialCode/Tutorial5/mymodel.cpp
removed src/TutorialCode/Tutorial5/mymodel.h
removed src/TutorialCode/Tutorial5/mymodel.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

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
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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
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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

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