EI/VirtualLeaf Changeset - 4d22d3755063 · Centrum Wiskunde & Informatica (CWI)

Changeset - 4d22d3755063

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Roeland Merks - 15 years ago 2010-10-14 11:53:43
roeland.merks@cwi.nl

Merged ChangeLog

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user: Roeland Merks <roeland.merks@cwi.nl>
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changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
changed src/ChangeLog

6 files changed with 269 insertions and 235 deletions:

data/leaves/ChangeLog

data/leaves/auxin_growth.xml

doc/v1.html

doc/v1.pdf

235

208

doc/v1.rst

src/ChangeLog

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data/leaves/ChangeLog

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 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* auxin_growth.xml: Changed export_fn_prefix to 'cell.'
 -10-08    <guravage@caterpie.sen.cwi.nl>
 	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* Added: tutorial3_init.xml
 	tutorial4_init.xml
 	tutorial5_init.xml
 	* Removed: bend.xml
 	circ.xml
 	explant.xml
 	init.xml
 	one_acc_point_van3.xml
 	one_acc_point_van3_growth.xml
 	one_acc_point_van3_growth2.xml
 	tissue.xml

data/leaves/auxin_growth.xml

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 <?xml version="1.0" encoding="UTF-8"?>
 <!--
   $Rev$:  Revision of last commit
   $Author$:  Author of last commit
   $Source$:  Source file
   $Date$:  Date of last commit
   This file is part of the Virtual Leaf.
   The Virtual Leaf is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
   The Virtual Leaf is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   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.
 -->
 <leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">
   <parameter>
     <par name="export_interval" val="1000"/>
-    <par name="export_fn_prefix" val="CELLDATA_"/>
+    <par name="export_fn_prefix" val="cell."/>
     <par name="arrowcolor" val="white"/>
     <par name="arrowsize" val="10"/>
     <par name="textcolor" val="red"/>
     <par name="cellnumsize" val="1"/>
     <par name="nodenumsize" val="1"/>
     <par name="node_mag" val="1"/>
     <par name="outlinewidth" val="1"/>
     <par name="cell_outline_color" val="forestgreen"/>
     <par name="resize_stride" val="10"/>
     <par name="T" val="1"/>
     <par name="lambda_length" val="100"/>
     <par name="lambda_celllength" val="0"/>
     <par name="target_length" val="60"/>
     <par name="cell_expansion_rate" val="10"/>
     <par name="cell_div_expansion_rate" val="10"/>
     <par name="auxin_dependent_growth" val="true"/>
     <par name="ode_accuracy" val="0.0001"/>
     <par name="mc_stepsize" val="0.4"/>
     <par name="mc_cell_stepsize" val="0.2"/>
     <par name="energy_threshold" val="1000"/>
     <par name="bend_lambda" val="0"/>
     <par name="alignment_lambda" val="0"/>
     <par name="rel_cell_div_threshold" val="2"/>
     <par name="rel_perimeter_stiffness" val="2"/>
     <par name="collapse_node_threshold" val="0.05"/>
     <par name="morphogen_div_threshold" val="0.2"/>
     <par name="morphogen_expansion_threshold" val="0.01"/>
     <par name="copy_wall" val="true"/>
     <par name="source" val="0"/>
     <par name="D">
       <valarray>
         <val v="1e-06"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="initval">
       <valarray>
         <val v="0"/>
         <val v="1"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="k1" val="1"/>
     <par name="k2" val="0.3"/>
     <par name="r" val="1"/>
     <par name="kr" val="1"/>
     <par name="km" val="1"/>
     <par name="Pi_tot" val="1"/>
     <par name="transport" val="0.36"/>
     <par name="ka" val="1"/>
     <par name="pin_prod" val="0"/>
     <par name="pin_prod_in_epidermis" val="0"/>
     <par name="pin_breakdown" val="0"/>
     <par name="pin_breakdown_internal" val="0.001"/>
     <par name="aux1prod" val="0.001"/>
     <par name="aux1prodmeso" val="0"/>
     <par name="aux1decay" val="0.001"/>
     <par name="aux1decaymeso" val="0.1"/>
     <par name="aux1transport" val="0.036"/>
     <par name="aux_cons" val="0"/>
     <par name="aux_breakdown" val="0.0001"/>
     <par name="kaux1" val="1"/>
     <par name="kap" val="1"/>
     <par name="leaf_tip_source" val="0.0001"/>
     <par name="sam_efflux" val="0.0001"/>
     <par name="sam_auxin" val="10"/>
     <par name="sam_auxin_breakdown" val="0"/>
     <par name="dt" val="0.1"/>
     <par name="rd_dt" val="10"/>
     <par name="datadir" val="auxin_growth"/>
     <par name="movie" val="true"/>
     <par name="nit" val="100000"/>
     <par name="maxt" val="1e+06"/>
     <par name="storage_stride" val="10"/>
     <par name="xml_storage_stride" val="500"/>
     <par name="rseed" val="-1"/>
     <par name="constituous_expansion_limit" val="16"/>
     <par name="vessel_inh_level" val="1"/>
     <par name="vessel_expansion_rate" val="0.25"/>
     <par name="d" val="0"/>
     <par name="e" val="0"/>
     <par name="f" val="0"/>
     <par name="c" val="0"/>
     <par name="mu" val="0"/>
     <par name="nu" val="0"/>
     <par name="rho0" val="0"/>
     <par name="rho1" val="0"/>
     <par name="c0" val="0"/>
     <par name="gamma" val="0"/>
     <par name="eps" val="0"/>
   </parameter>
   <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;
 #include &lt;sstream&gt;
 #include &lt;cstring&gt;
 #include &lt;functional&gt;
 #include &lt;getopt.h&gt;
 #include &lt;cerrno&gt;
 #include "mesh.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "cellitem.h"
 #include "canvas.h"
 #include "cell.h"
 #include "output.h"
 #include &lt;qwidget.h&gt;
 #include &lt;q3process.h&gt;
 #include &lt;qapplication.h&gt;
 #include &lt;QDesktopWidget&gt;
 #include &lt;QGraphicsScene&gt;
 #include &lt;QMessageBox&gt;
 //Added by qt3to4:
 #include &lt;QMouseEvent&gt;
 #include &lt;unistd.h&gt;
 #include &lt;q3textstream.h&gt;
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include &lt;QPalette&gt;
 #include &lt;QBrush&gt;
 #include &lt;QToolTip&gt;
 #include "simplugin.h"
 #include "testplugin.h"
 /* #define _xstr_(s) _str_(s)
 #define _str_(s) #s
 #include _xstr_(REACTIONS_HEADER)
 */
 extern Parameter par;
 MainBase *main_window = 0;
 double auxin_account = 0.;
 TestPlugin *plugin = new TestPlugin();
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
   void operator() (const Node &amp;n) const
+  {
     cerr &lt;&lt; n.Index() &lt;&lt; ": " &lt;&lt; n &lt;&lt;  endl;
+  }
 };
 class EdgeSource {
 public:
   void operator() (Cell &amp;c) {
     if (c.AtBoundaryP()) {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is a source cell.\n";
       c.SetSource(0,par.source);
     } else {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is _not_ a source cell.\n";
+    }
+  }
 };
 class CellInfo {
 public:
   void operator() (Cell &amp;c,std::ostream &amp;os) const {
     os &lt;&lt; "Cell " &lt;&lt; c.index &lt;&lt; " says: " &lt;&lt; endl;
     os &lt;&lt; "c.nodes.size() = " &lt;&lt; c.nodes.size() &lt;&lt; endl;
     for (list&lt;Node *&gt;::iterator i=c.nodes.begin();
 	 i!=c.nodes.end();
 	 i++) {
       cerr &lt;&lt; (*i)-&gt;Index() &lt;&lt; " ";
+    }
     cerr &lt;&lt; endl;
+  }
 };
 double PINSum(Cell &amp;c) {
 	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls&lt;double&gt;( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &amp;c,QGraphicsScene &amp;canvas, MainBase &amp;m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() &amp;&amp; !m.HideCellsP())
 	if (m.ShowToolTipsP()) {
 	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\n" + c.printednodelist();
 	  c.Draw(&amp;canvas, info_string);
 	} else {
 	  c.Draw(&amp;canvas);
+	}
       if (m.ShowCentersP())
 	c.DrawCenter(&amp;canvas);
     if (m.ShowFluxesP())
 	c.DrawFluxes(&amp;canvas, par.arrowsize);
+       }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride) {
   clear();
   static int count=0;
   if (resize_stride) {
     if ( !((++count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &amp;Node::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawAxis), &amp;canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawStrain), &amp;canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::Draw ), &amp;canvas ) );
 	if (ShowApoplastsP())
 		mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::DrawApoplast ), &amp;canvas ) );
 	if (ShowMeshP())
     mesh.DrawNodes(&amp;canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&amp;canvas);
 	if ( ( batch || MovieFramesP() )) {
 		static int frame = 0;
 		// frame numbers are sequential for the most frequently written file type.
 		// for the less frequently written file type they match the other type
 		if (!(count%par.storage_stride) )  {
 			stringstream fname;
 			fname &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			/*
 			 fname &lt;&lt; frame &lt;&lt; ".pdf";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "PDF");
 			*/
 			fname &lt;&lt; frame &lt;&lt; ".jpg";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "JPEG",1024,768);
+		}
 		if (!(count%par.xml_storage_stride)) {
 			stringstream fname;
 			fname &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			fname &lt;&lt; frame &lt;&lt; ".xml";
 			if (par.xml_storage_stride &lt; par.storage_stride) {
 				frame++;
+			}
 			// Write XML file every ten plot steps
 			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+		}
+	}
+}
 void Cell::Flux(double *flux, double *D)  {
   // loop over cell edges
   for (int c=0;c&lt;Cell::nchem;c++) flux[c]=0.;
   for (list&lt;Wall *&gt;::iterator i=walls.begin();
        i!=walls.end();
        i++) {
     // leaf cannot take up chemicals from environment ("no flux boundary")
     if ((*i)-&gt;c2-&gt;BoundaryPolP()) continue;
     // flux depends on edge length and concentration difference
     for (int c=0;c&lt;Cell::nchem;c++) {
       double phi = (*i)-&gt;length * ( D[c] ) * ( (*i)-&gt;c2-&gt;chem[c] - chem[c] );
       if ((*i)-&gt;c1!=this) {
 	cerr &lt;&lt; "Warning, bad cells boundary: " &lt;&lt; (*i)-&gt;c1-&gt;index &lt;&lt; ", " &lt;&lt; index &lt;&lt; endl;
+      }
       flux[c] += phi;
+    }
+  }
+}
 INIT {
 	if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &amp;settings);
     main_window-&gt;XMLReadSettings(settings);
     xmlFree(settings);
     main_window-&gt;UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
   } else {
 	  Cell &amp;circle=mesh.CircularCell(0,0,10,10);
     circle.SetTargetArea(circle.CalcArea());
 	  mesh.SetBaseArea();
 	// clean up chemicals
 	  for (int c=0; c&lt;Cell::NChem(); c++) {
 		  circle.SetChemical(c, 0.);
+      }
+  }
+}
 TIMESTEP {
   static int i=0;
   static int t=0;
   static int ncells;
   if (!batch) {
     UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);
+  }
   ncells=mesh.NCells();
   double dh;
   if(DynamicCellsP()) {
     dh = mesh.DisplaceNodes();
     // Only allow for node insertion, cell division and cell growth
     // if the system has equillibrized
     // i.e. cell wall tension equillibrization is much faster

doc/v1.html

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@@ @@ -163,451 +163,441 @@ img.align-left, .figure.align-left{ @@
   margin-right: 1em }
 img.align-right, .figure.align-right {
   clear: right ;
   float: right ;
   margin-left: 1em }
 .align-left {
   text-align: left }
 .align-center {
   clear: both ;
   text-align: center }
 .align-right {
   text-align: right }
 /* reset inner alignment in figures */
 div.align-right {
   text-align: left }
 /* div.align-center * { */
 /*   text-align: left } */
 ol.simple, ul.simple {
   margin-bottom: 1em }
 ol.arabic {
   list-style: decimal }
 ol.loweralpha {
   list-style: lower-alpha }
 ol.upperalpha {
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 ol.lowerroman {
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 p.attribution {
   text-align: right ;
   margin-left: 50% }
 p.caption {
   font-style: italic }
 p.credits {
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   font-size: smaller }
 p.label {
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   font-weight: bold ;
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 pre.address {
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 pre.literal-block, pre.doctest-block {
   margin-left: 2em ;
   margin-right: 2em }
 span.classifier {
   font-family: sans-serif ;
   font-style: oblique }
 span.classifier-delimiter {
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 span.interpreted {
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 span.option {
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 span.pre {
   white-space: pre }
 span.problematic {
   color: red }
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   /* font-size relative to parent (h1..h6 element) */
   font-size: 80% }
 table.citation {
   border-left: solid 1px gray;
   margin-left: 1px }
 table.docinfo {
   margin: 2em 4em }
 table.docutils {
   margin-top: 0.5em ;
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 table.footnote {
   border-left: solid 1px black;
   margin-left: 1px }
 table.docutils td, table.docutils th,
 table.docinfo td, table.docinfo th {
   padding-left: 0.5em ;
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 table.docutils th.field-name, table.docinfo th.docinfo-name {
   font-weight: bold ;
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   white-space: nowrap ;
   padding-left: 0 }
 h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
 h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
   font-size: 100% }
 ul.auto-toc {
   list-style-type: none }
 </style>
 </head>
 <body>
 <div class="header">
 ###Title###
 <hr class="header"/>
 </div>
 <div class="document" id="the-virtual-leaf">
 <h1 class="title">The Virtual Leaf</h1>
 <div class="section" id="friday-11-june-2010">
 <h1>Friday 11 June 2010</h1>
 <p>Issues:</p>
 <blockquote>
 <ol class="arabic">
 <li><p class="first">Every class that has an association or composition eventually will
 need its own custom view page template, e.g. sed_view. For the moment
 I have set the default view for these classes to dev_view ( a copy of
 base_view ).</p>
 </li>
 <li><p class="first">An association in UML is cast as a ReferenceField in the resulting
 class schema. Open the association and add the widget:label tag to
 the class that is being associated.</p>
 </li>
 <li><p class="first">The default description text for a class should be a informative
 description of the class, not the instance, derived from the
 SED-ML manual.</p>
 </li>
 <li><p class="first">Apply 'searchable' tags to the appropriate class attributes.</p>
 </li>
 <li><p class="first">I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
 this work?</p>
 </li>
 <li><p class="first">What should be added to our implementation of SED-ML to make it
 more than merely a mirror image of the SED-ML XML format?</p>
 <blockquote>
 <ol class="loweralpha simple">
 <li>The ability to attach files at various points, e.g. parameter files.</li>
 <li>Additional output types, e.g. animations.</li>
 <li>Custom page templates</li>
 <li>Custom search form</li>
 <li>Custom catalog indexes</li>
 <li>Custom portlet(s)</li>
 <li>Custom viewlet(s)</li>
 </ol>
 </blockquote>
 </li>
 </ol>
 </blockquote>
 </div>
 <div class="section" id="friday-24-september-2010">
 <h1>Friday 24 September 2010</h1>
 <dl class="docutils">
 <dt>To Do:</dt>
 <dd><ol class="first last arabic simple">
 <li>Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.</li>
 <li>Create a vleaf mailing list (Henk).</li>
 </ol>
 </dd>
 </dl>
 <p>Found an article on SBRML - a markup language for associating systems
 biology data with models. At a glance the schema seems bigger than
 SED-ML's, but SBRML appears to be SBML specific.</p>
 </div>
 <div class="section" id="monday-27-september-2010">
 <h1>Monday 27 September 2010</h1>
 <p>Spoke with Chris about publishing the Mercurial repositories and
 deploying Plone. Both can be accomplished in their own project space
 on a server in the DMZ. Chris said he would supply me with login
 credentials for both accounts. I will install Plone and Chris (or
 Maarten) will help me configure Apache/nginx and Varnish. Chris will
 install the required Mercurial packages; after which I can clone the
 repositories to their new home.</p>
 </div>
 <div class="section" id="tuesday-5-october-20010">
 <h1>Tuesday 5 October 20010</h1>
 <div class="section" id="tutorial0-pro">
 <h2>tutorial0.pro</h2>
 <p>Added simplugin.h to list of header files. NB: this is the only
 tutorial in which simplugin.h appears.</p>
 </div>
 <div class="section" id="auxingrowthplugin-h">
 <h2>auxingrowthplugin.h</h2>
 <p>Declared, and defined, a virtual function named <tt class="docutils literal">DefaultLeafML()</tt>
 which merely returns a QString naming a LeafML filename sans path.</p>
 </div>
 <div class="section" id="virtualleaf-cpp">
 <h2>VirtualLeaf.cpp</h2>
 <p>Moved <tt class="docutils literal"><span class="pre">Cell::SetMagnification()</span></tt> and <tt class="docutils literal"><span class="pre">Cell::SetOffset()</span></tt> from
 <tt class="docutils literal">main()</tt> to <tt class="docutils literal"><span class="pre">MainBase::Init()</span></tt>.</p>
 </div>
 <div class="section" id="canvas-h">
 <h2>canvas.h</h2>
 <p>Declare <tt class="docutils literal">exportCellData()</tt>.</p>
 </div>
 <div class="section" id="canvas-cpp">
 <h2>canvas.cpp</h2>
 <p>Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - <tt class="docutils literal"><span class="pre">Main::exportCellData()</span></tt>:</p>
 <pre class="literal-block">
 void Main::exportCellData(void) {
   QFile file(&quot;areas.csv&quot;);
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &amp;file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
+  }
+}
 </pre>
 </div>
 <div class="section" id="mesh-h">
 <h2>mesh.h</h2>
 <p>Include <tt class="docutils literal">&lt;QTextStream&gt;</tt></p>
 <p>Set the boundary_poloygon pointer to zero in the class constructor,
 and delete it, if it exists, in the class destructor.</p>
 <p>Declare <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>:</p>
 <pre class="literal-block">
 double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);
 void CSVExportCellData(QTextStream &amp;csv_stream) const;
 void CSVExportMeshData(QTextStream &amp;csv_stream);
 </pre>
 </div>
 <div class="section" id="mesh-cpp">
 <h2>mesh.cpp</h2>
 <p>In <tt class="docutils literal"><span class="pre">mesh::clear()</span></tt>, delete the boundary_polygon only if the pointer hasn't been assigned:</p>
 <pre class="literal-block">
 if (boundary_polygon) {
    delete boundary_polygon;
    boundary_polygon=0;
+ }
 </pre>
 <p>Ditto for <tt class="docutils literal"><span class="pre">mesh::clean()</span></tt>.</p>
 <p>Define the code for <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>.</p>
 </div>
 <div class="section" id="modelcatalogue-cpp">
 <h2>modelcatalogue.cpp</h2>
 <p>In <tt class="docutils literal">InstallModel()</tt>, find and load the default LeafML file.</p>
 </div>
 <div class="section" id="simplugin-h">
 <h2>simplugin.h</h2>
 <p>Declare <tt class="docutils literal">DefaultLeafML()</tt>:</p>
 <pre class="literal-block">
 // Default LeafML-file to be read after model startup
 virtual QString DefaultLeafML(void);
 </pre>
 </div>
 <div class="section" id="simplugin-cpp">
 <h2>simplugin.cpp</h2>
 <p>Define <tt class="docutils literal">DefaultLeafML()</tt>. Returns an empty <tt class="docutils literal">QString</tt>:</p>
 <pre class="literal-block">
 QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
 </pre>
 </div>
 <div class="section" id="xmlwrite-cpp">
 <h2>xmlwrite.cpp</h2>
 <p>In <tt class="docutils literal"><span class="pre">Mesh::XMLReadCells()</span></tt> - Delete the boundary_ploygon only if its
 pointer has been assigned.</p>
 </div>
 </div>
 <div class="section" id="wednesday-6-october-2010">
 <h1>Wednesday 6 October 2010</h1>
 <p>Wrote Simon van Mourik about his missing libiconv-2.dll.</p>
 </div>
 <div class="section" id="thursday-7-october-2010">
 <h1>Thursday 7 October 2010</h1>
 <p>Added a Q3FileDialog in <tt class="docutils literal"><span class="pre">canvas.cpp:Main::exportCellData(void)</span></tt> to
 choose where to write the exported cell data.</p>
 </div>
 <div class="section" id="friday-8-october-2010">
 <h1>Friday 8 October 2010</h1>
 <p>Added new parameters to control perodic cell exprt data.</p>
 <p>Added code to relize perodic cell export.</p>
 </div>
 <div class="section" id="monday-11-october-2010">
 <h1>Monday 11 October 2010</h1>
 <div class="section" id="mercurial-hooks">
 <h2>Mercurial hooks</h2>
 <p>Tried several alternatives for Mercurial's <tt class="docutils literal">pretxnchangegroup.forbid_2heads</tt> hook.</p>
 <ol class="arabic simple">
 <li><a class="reference external" href="http://bitbucket.org/dgc/headcount">http://bitbucket.org/dgc/headcount</a>: <strong>Headcount</strong> <tt class="docutils literal">ui</tt> complains of a missing data member</li>
 <li><a class="reference external" href="http://stackoverflow.com/questions/1705921/useful-mercurial-hooks">http://stackoverflow.com/questions/1705921/useful-mercurial-hooks</a>: <strong>forbid2_heads.py</strong> doesn't load</li>
 <li><a class="reference external" href="http://davidherron.com/node/961">http://davidherron.com/node/961</a>: <strong>forbid2_heads.sh</strong> works as advertised</li>
 </ol>
 </div>
 <div class="section" id="mercurial-repositories">
 <h2>Mercurial Repositories</h2>
 <p>Tried to install Rhode Code from: <a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>.</p>
 <ol class="arabic simple">
 <li><a class="reference external" href="http://bitbucket.org/marcinkuzminski/rhodecode">http://bitbucket.org/marcinkuzminski/rhodecode</a></li>
 <li><a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc3">http://pypi.python.org/pypi/RhodeCode/1.0.0rc3</a></li>
 <li><a class="reference external" href="http://hg.python-works.com">http://hg.python-works.com</a> (demo,demo)</li>
 <li><a class="reference external" href="http://bitbucket.org/bfrog/cutehg">http://bitbucket.org/bfrog/cutehg</a></li>
 <li><a class="reference external" href="http://pypi.python.org/pypi/SIP">http://pypi.python.org/pypi/SIP</a>, <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>
 <li><a class="reference external" href="http://pypi.python.org/pypi/PyQt">http://pypi.python.org/pypi/PyQt</a></li>
 <li><a class="reference external" href="http://ask.github.com/celery">http://ask.github.com/celery</a></li>
 </ol>
 <p>All goes tolerably until you tick in the url; at which point RhodeCode complains that:</p>
 <pre class="literal-block">
 Exception happened during processing of request from ('127.0.0.1', 35803)
 Traceback (most recent call last):
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py&quot;, line 320, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py&quot;, line 615, in __init__
    self.handle()
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 442, in handle
    BaseHTTPRequestHandler.handle(self)
  File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py&quot;, line 329, in handle
    self.handle_one_request()
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 437, in handle_one_request
    self.wsgi_execute()
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 287, in wsgi_execute
    self.wsgi_start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py&quot;, line 130, in __call__
    return self.apps[-1](environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py&quot;, line 379, in __call__
    app_iter = self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py&quot;, line 33, in __call__
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py&quot;, line 163, in __call__
    self.app, new_environ, catch_exc_info=True)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py&quot;, line 48, in call_wsgi_application
    app_iter = application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py&quot;, line 156, in __call__
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py&quot;, line 55, in __call__
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py&quot;, line 152, in __call__
    return self.wrap_app(environ, session_start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py&quot;, line 131, in __call__
    response = self.app(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 98, in __call__
    self.setup_app_env(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 203, in setup_app_env
    pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py&quot;, line 165, in _get_translator
    raise LanguageError('IOError: %s' % ioe)
 LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
 </pre>
 </div>
 <div class="section" id="re-install">
 <h2>RE-INSTALL</h2>
 <blockquote>
 <ol class="arabic simple">
 <li>easy_install mercurial</li>
 <li>mkdir src</li>
 <li>cd src</li>
 <li>hg clone <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>
 <li>cd sip</li>
 <li>python build.py prepare</li>
 <li>python configure.py</li>
 <li>make</li>
 <li>make install</li>
 </ol>
 </blockquote>
 <div class="system-message">
 <p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">v1.rst</tt>, line 295)</p>
 Block quote ends without a blank line; unexpected unindent.</div>
 <ol class="arabic simple" start="10">
 <li>cd ..</li>
-<li>curl <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
+<li>wget <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
 <li>tar xzf PyQt-x11-gpl-4.7.7</li>
 <li>cd PyQt-x11-gpl-4.7.7</li>
 <li>python configure.py</li>
 <li>make</li>
 <li>make install</li>
 <li>cd ..</li>
 <li>hg clone <a class="reference external" href="https://litsol&#64;bitbucket.org/bfrog/cutehg">https://litsol&#64;bitbucket.org/bfrog/cutehg</a></li>
 <li>cd cutehg</li>
 <li>python setup.py build</li>
 <li>python setup.py install</li>
 <li>cd ..</li>
 <li>easy_install rhodecode, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc2">http://pypi.python.org/pypi/RhodeCode/1.0.0rc2</a></li>
 </ol>
 <div class="system-message">
 <p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">v1.rst</tt>, line 307)</p>
 Enumerated list ends without a blank line; unexpected unindent.</div>
 <p>22. cd ..
 . easy_install rhodecode, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc2">http://pypi.python.org/pypi/RhodeCode/1.0.0rc2</a></p>
 <p>This procedure fails as before.</p>
 <p>However, upon inspection I saw that the i18n directory was missing
 from my build but present in the rhodecode clone from bitbucket. While
 I think that the <tt class="docutils literal">easy_install rhodecode</tt> invocation is necessary to
 install the various subsidiary packages, moving the cloned rhodecode
 into the site-packages directory seems to have made most functionality
 work. e.g. graphical logs and diff highlighting.</p>
 </div>
 </div>
 <div class="section" id="tuesday-12-october-2010">
 <h1>Tuesday 12 October 2010</h1>
 <div class="section" id="rhodecode">
 <h2>RhodeCode</h2>
 <p>I think that if Chris can install RhodeCode, I can serve individual
 instance from my home directory.</p>
 </div>
 <div class="section" id="sed-ml-l1v1rc1">
 <h2>SED-ML L1V1RC1</h2>
 <p>Walking through the new SED-ML schema I see that they've dropped the
 generic simulation class and added AddXML and RemoveXML model change
 classes. Adding several more SED-ML examples for the symposium might
 still be justified - though they become obsolete the moment I
 introduce the new schema changes.</p>
 </div>
 </div>
 </div>
 <div class="footer">
 <hr class="footer" />
 ###Page###
 </div>
 </body>
 </html>

doc/v1.pdf

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doc/v1.rst

➞

Show inline comments

 .. header::
    ###Title###
 .. footer::
    ###Page###
 ================
 The Virtual Leaf
 ================
 Friday 11 June 2010
 -------------------
 Issues:
 . Every class that has an association or composition eventually will
     need its own custom view page template, e.g. sed_view. For the moment
     I have set the default view for these classes to dev_view ( a copy of
     base_view ).
 . An association in UML is cast as a ReferenceField in the resulting
     class schema. Open the association and add the widget:label tag to
     the class that is being associated.
 . The default description text for a class should be a informative
     description of the class, not the instance, derived from the
     SED-ML manual.
 . Apply 'searchable' tags to the appropriate class attributes.
 . I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
     this work?
 . What should be added to our implementation of SED-ML to make it
     more than merely a mirror image of the SED-ML XML format?
      a. The ability to attach files at various points, e.g. parameter files.
      b. Additional output types, e.g. animations.
      c. Custom page templates
      d. Custom search form
      e. Custom catalog indexes
      f. Custom portlet(s)
      g. Custom viewlet(s)
 Friday 24 September 2010
 ------------------------
 To Do:
 . Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.
 . Create a vleaf mailing list (Henk).
 Found an article on SBRML - a markup language for associating systems
 biology data with models. At a glance the schema seems bigger than
 SED-ML's, but SBRML appears to be SBML specific.
 Monday 27 September 2010
 ------------------------
 Spoke with Chris about publishing the Mercurial repositories and
 deploying Plone. Both can be accomplished in their own project space
 on a server in the DMZ. Chris said he would supply me with login
 credentials for both accounts. I will install Plone and Chris (or
 Maarten) will help me configure Apache/nginx and Varnish. Chris will
 install the required Mercurial packages; after which I can clone the
 repositories to their new home.
 Tuesday 5 October 20010
 -----------------------
 tutorial0.pro
 +++++++++++++
 Added simplugin.h to list of header files. NB: this is the only
 tutorial in which simplugin.h appears.
 auxingrowthplugin.h
 +++++++++++++++++++
 Declared, and defined, a virtual function named ``DefaultLeafML()``
 which merely returns a QString naming a LeafML filename sans path.
 VirtualLeaf.cpp
 +++++++++++++++
 Moved ``Cell::SetMagnification()`` and ``Cell::SetOffset()`` from
 ``main()`` to ``MainBase::Init()``.
 canvas.h
 ++++++++
 Declare ``exportCellData()``.
 canvas.cpp
 ++++++++++
 Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - ``Main::exportCellData()``::
   void Main::exportCellData(void) {
     QFile file("areas.csv");
     if ( file.open( IO_WriteOnly ) ) {
       QTextStream stream( &file );
       mesh.CSVExportCellData(stream);
       mesh.CSVExportMeshData(stream);
       file.close();
+    }
+  }
 mesh.h
 ++++++
 Include ``<QTextStream>``
 Set the boundary_poloygon pointer to zero in the class constructor,
 and delete it, if it exists, in the class destructor.
 Declare ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``::
   double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);
   void CSVExportCellData(QTextStream &csv_stream) const;
   void CSVExportMeshData(QTextStream &csv_stream);
 mesh.cpp
 ++++++++
 In ``mesh::clear()``, delete the boundary_polygon only if the pointer hasn't been assigned::
  if (boundary_polygon) {
     delete boundary_polygon;
     boundary_polygon=0;
+  }
 Ditto for ``mesh::clean()``.
 Define the code for ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``.
 modelcatalogue.cpp
 ++++++++++++++++++
 In ``InstallModel()``, find and load the default LeafML file.
 simplugin.h
 +++++++++++
 Declare ``DefaultLeafML()``::
   // Default LeafML-file to be read after model startup
   virtual QString DefaultLeafML(void);
 simplugin.cpp
 +++++++++++++
 Define ``DefaultLeafML()``. Returns an empty ``QString``::
  QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
 xmlwrite.cpp
 ++++++++++++
 In ``Mesh::XMLReadCells()`` - Delete the boundary_ploygon only if its
 pointer has been assigned.
 Wednesday 6 October 2010
 ------------------------
 Wrote Simon van Mourik about his missing libiconv-2.dll.
 Thursday 7 October 2010
 -----------------------
 Added a Q3FileDialog in ``canvas.cpp:Main::exportCellData(void)`` to
 choose where to write the exported cell data.
 Friday 8 October 2010
 ---------------------
 Added new parameters to control perodic cell exprt data.
 Added code to relize perodic cell export.
 Monday 11 October 2010
 ----------------------
 Mercurial hooks
 +++++++++++++++
 Tried several alternatives for Mercurial's ``pretxnchangegroup.forbid_2heads`` hook.
 . http://bitbucket.org/dgc/headcount: **Headcount** ``ui`` complains of a missing data member
 . http://stackoverflow.com/questions/1705921/useful-mercurial-hooks: **forbid2_heads.py** doesn't load
 . http://davidherron.com/node/961: **forbid2_heads.sh** works as advertised
 Mercurial Repositories
 ++++++++++++++++++++++
 Tried to install Rhode Code from: http://packages.python.org/RhodeCode.
 . http://bitbucket.org/marcinkuzminski/rhodecode
 . http://packages.python.org/RhodeCode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc3
 . http://hg.python-works.com (demo,demo)
 . http://bitbucket.org/bfrog/cutehg
 . http://pypi.python.org/pypi/SIP, http://www.riverbankcomputing.com/hg/sip
 . http://pypi.python.org/pypi/PyQt
 . http://ask.github.com/celery
 All goes tolerably until you tick in the url; at which point RhodeCode complains that::
  Exception happened during processing of request from ('127.0.0.1', 35803)
  Traceback (most recent call last):
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
     self.finish_request(request, client_address)
   File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 320, in finish_request
     self.RequestHandlerClass(request, client_address, self)
   File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 615, in __init__
     self.handle()
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle
     BaseHTTPRequestHandler.handle(self)
   File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py", line 329, in handle
     self.handle_one_request()
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request
     self.wsgi_execute()
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
     self.wsgi_start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py", line 130, in __call__
     return self.apps[-1](environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py", line 379, in __call__
     app_iter = self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py", line 33, in __call__
     return self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py", line 163, in __call__
     self.app, new_environ, catch_exc_info=True)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py", line 48, in call_wsgi_application
     app_iter = application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py", line 156, in __call__
     return self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py", line 55, in __call__
     return self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py", line 152, in __call__
     return self.wrap_app(environ, session_start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py", line 131, in __call__
     response = self.app(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 98, in __call__
     self.setup_app_env(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 203, in setup_app_env
     pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py", line 165, in _get_translator
     raise LanguageError('IOError: %s' % ioe)
  LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
 RE-INSTALL
 ++++++++++
 . easy_install mercurial
 . mkdir src
 . cd src
 . hg clone http://www.riverbankcomputing.com/hg/sip
 . cd sip
 . python build.py prepare
 . python configure.py
 . make
 . make install
 . easy_install mercurial
 . mkdir src
 . cd src
 . hg clone http://www.riverbankcomputing.com/hg/sip
 . cd sip
 . python build.py prepare
 . python configure.py
 . make
 . make install
 . cd ..
-. curl http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
+. wget http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
 . tar xzf PyQt-x11-gpl-4.7.7
 . cd PyQt-x11-gpl-4.7.7
 . python configure.py
 . make
 . make install
 . cd ..
 . hg clone https://litsol@bitbucket.org/bfrog/cutehg
 . cd cutehg
 . python setup.py build
 . python setup.py install
 . cd ..
-. easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
+. easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
 This procedure fails as before.
 However, upon inspection I saw that the i18n directory was missing
 from my build but present in the rhodecode clone from bitbucket. While
 I think that the ``easy_install rhodecode`` invocation is necessary to
 install the various subsidiary packages, moving the cloned rhodecode
 into the site-packages directory seems to have made most functionality
 work. e.g. graphical logs and diff highlighting.
 Tuesday 12 October 2010
 -----------------------
 RhodeCode
 +++++++++
 I think that if Chris can install RhodeCode, I can serve individual
 instance from my home directory.
 SED-ML L1V1RC1
 ++++++++++++++
 Walking through the new SED-ML schema I see that they've dropped the
 generic simulation class and added AddXML and RemoveXML model change
 classes. Adding several more SED-ML examples for the symposium might
 still be justified - though they become obsolete the moment I
 introduce the new schema changes.
 Wednesday 13 October 2010
 -------------------------
 Tweaked ``.bashrc`` and ``virtualenvwrapper.sh`` to facilitate
 virtualenv and virtualenvwrapper - many unbound variables!
 Pushed recent changes to repository from where Roeland can retrieve
 and test them.
 OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.

src/ChangeLog

➞

Show inline comments

 -10-14    <merks@cwi.nl>
 	* 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.
 -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().
 -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.
 -10-07    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire
 	where to write the exportCellData.
 -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.
 -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.
 -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.
 -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.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (tutorials): Add tutorials target.
 -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.
 -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.
 -06-17    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed perl references.
 	* libplugin.pro: Ditto.
 -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.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -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
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

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