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 260 insertions and 226 deletions:

data/leaves/ChangeLog

data/leaves/auxin_growth.xml

doc/v1.html

doc/v1.pdf

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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

data/leaves/auxin_growth.xml

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@@ @@ -18,25 +18,25 @@ @@
   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"/>

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@@ @@ -535,59 +535,49 @@ Traceback (most recent call last): @@
    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">

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doc/v1.rst

➞

Show inline comments

@@ @@ -284,37 +284,37 @@ 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
 . 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.
@@ @@ -330,18 +330,23 @@ 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

@@ @@ -2,24 +2,32 @@ 2010-10-14 <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.

0 comments (0 inline, 0 general)