xap/compucell3d: Added compucell3d-20180916.

xap/compucell3d/CompuCell3D-20180916-fix-vtk7-gettuplevalue.patch

@@ -0,0 +1,28 @@
+diff -Naur CompuCell3D-20180916.orig/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp CompuCell3D-20180916/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp
+--- CompuCell3D-20180916.orig/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp	2018-07-23 01:30:09.000000000 +0100
++++ CompuCell3D-20180916/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp	2018-09-16 17:02:36.870316092 +0100
+@@ -655,7 +655,7 @@
+ 		for(pt.y =0 ; pt.y<fieldDim.y ; ++pt.y)
+ 			for(pt.x =0 ; pt.x<fieldDim.x ; ++pt.x){
+ 
+-				fieldArray->GetTupleValue(offset,tuple);
++				fieldArray->GetTypedTuple(offset,tuple);
+ 
+ // 				(*fieldPtr)[pt.x][pt.y][pt.z]=Coordinates3D<float>(tuple[0],tuple[1],tuple[2]) ;
+                                 
+@@ -789,7 +789,7 @@
+ 					if(mitr!=fieldPtr->end()){
+ 						;
+ 					}else{
+-						fieldArray->GetTupleValue(offset,tuple);
++						fieldArray->GetTypedTuple(offset,tuple);
+ 						cerr<<"inserting "<<Coordinates3D<float>(tuple[0],tuple[1],tuple[2])<<endl;
+ 						fieldPtr->insert(make_pair(cell,Coordinates3D<float>(tuple[0],tuple[1],tuple[2])));
+ 						
+@@ -801,4 +801,4 @@
+ 
+ 	fieldDataReader->Delete();
+ 	return true;
+-}
+\ No newline at end of file
++}

xap/compucell3d/compucell3d.SlackBuild

@@ -0,0 +1,144 @@
+#!/bin/bash
+# Build script for Slackware
+# Copyright (C) 2018 Damien Goutte-Gattat
+#
+# Redistribution and use of this script, with or without modifications,
+# is permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
+# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
+#
+# Latest CompuCell3D sourcecode is available at:
+# <http://www.compucell3d.org/>.
+#
+# Depends: l/PyQt5, l/vtk, l/pyqtgraph, l/qscintilla
+
+# Source package infos
+NAMESRC=${NAMESRC:-CompuCell3D}
+VERSION=${VERSION:-20180916}
+REPOSITORY=${REPOSITORY:-https://github.com/CompuCell3D/CompuCell3D.git}
+COMMIT=${COMMIT:-48c9ca56be7ad07cebcfd5a4048fa25bd0ae8854}
+ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
+
+# Build infos
+NAMEPKG=${NAMEPKG:-compucell3d}
+BUILD=${BUILD:-1GGD}
+ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
+JOBS=${JOBS:-1}
+EXT=${EXT:-txz}
+
+# Directories
+TMP=${TMP:-/tmp}
+OUT=${OUT:-$TMP/build}
+PKG=${PKG:-$OUT/$NAMEPKG}
+CWD=$(pwd)
+
+set -e  # Quit if a command returns non-zero
+
+# Sanity checks
+if [ $UID -eq 0 ]; then
+    echo "You should NOT run this script as ROOT!"
+    exit 1
+fi
+if [ ! -d $TMP ]; then
+    echo "$TMP does not exists or is not a directory!"
+    exit 1
+fi
+
+# Compilation flags
+LIBDIRSUFFIX=""
+case "$ARCH" in
+i?86)
+    CPUOPT="-O2 -march=$ARCH -mtune=i686"
+    ;;
+x86_64)
+    CPUOPT="-O2 -fPIC"
+    LIBDIRSUFFIX="64"
+    ;;
+*)
+    CPUOPT="-O2"
+    ;;
+esac
+
+# Get and verify the source archive
+NAME=$NAMESRC-$VERSION
+if [ ! -r $ARCHIVE ]; then
+    git clone $REPOSITORY CompuCell3D
+    cd CompuCell3D
+    git archive --prefix=$NAME/ $COMMIT | gzip -c > ../$ARCHIVE
+    cd ..
+    rm -rf CompuCell3D
+fi
+
+# Compile
+cd $TMP
+echo "Building $ARCHIVE..."
+tar xf $CWD/$ARCHIVE
+cd $NAME
+# Allow compile with VTK >= 7
+patch -p 1 < $CWD/CompuCell3D-20180916-fix-vtk7-gettuplevalue.patch
+mkdir CompuCell3D/build && cd CompuCell3D/build
+cmake \
+  -DCMAKE_BUILD_TYPE=Release \
+  -DCMAKE_INSTALL_PREFIX=/opt/compucell3d \
+  -DBUILD_PYINTERFACE=ON \
+  -DBUILD_QT_WRAPPERS=ON \
+  -DCMAKE_CXX_FLAGS="$CPUOPT -std=c++11 -DVTK6" \
+  ..
+make -j $JOBS
+make install/strip DESTDIR=$PKG
+cd ..
+
+# Install launchers
+install -D -m 755 $CWD/compucell3d.sh $PKG/usr/bin/compucell3d
+install    -m 755 $CWD/twedit++.sh    $PKG/usr/bin/twedit++
+
+# Install the documentation
+mkdir -p $PKG/usr/doc/$NAME
+install -m 644 ChangeLog.txt README-Linux.txt ReleaseNotes.rst \
+  docs/CompuCell3D_release_notes.pdf  $PKG/usr/doc/$NAME
+
+# Install desktop files
+install -D -m 644 $CWD/compucell3d.desktop $PKG/usr/share/applications/compucell3d.desktop
+install    -m 644 $CWD/twedit++.desktop    $PKG/usr/share/applications/twedit++.desktop
+
+# Copy slack-desc and doinst.sh files
+install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
+install    -m 755 $CWD/doinst.sh  $PKG/install/doinst.sh
+
+# Add dependency infos
+cat <<EOF > $PKG/install/slack-required
+PyQt5
+vtk
+pyqtgraph
+qscintilla
+EOF
+
+# Package the tree
+cd $PKG
+mkdir -p $OUT
+PACKAGING="
+chown root:root . -R
+/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
+rm -rf $PKG
+rm -rf $TMP/$NAME
+"
+if type -p fakeroot ; then
+    echo "$PACKAGING" | fakeroot
+else
+    su -c "$PACKAGING"
+fi

xap/compucell3d/compucell3d.desktop

@@ -0,0 +1,7 @@
+[Desktop Entry]
+Name=CompuCell3D
+Comment=Cell modeling environment
+Type=Application
+Categories=Education;Science;
+Exec=/usr/bin/compucell3d
+Terminal=false

xap/compucell3d/compucell3d.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+exec /opt/compucell3d/compucell3d.sh $@

xap/compucell3d/doinst.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+if [ -x /usr/bin/update-desktop-database ]; then
+    /usr/bin/update-desktop-database ./usr/share/applications >/dev/null 2>&1
+fi

xap/compucell3d/slack-desc

@@ -0,0 +1,12 @@
+           |-----handy-ruler-----------------------------------------------------|
+compucell3d: compucell3d (cell modeling environment)
+compucell3d: 
+compucell3d: CompuCell3D is a flexible scriptable modeling environment, which
+compucell3d: allows the rapid construction of sharable Virtal Tissue in-silico
+compucell3d: simulations of a wide variety of multi-scale, multi-cellular
+compucell3d: problems including angiogenesis, bacterial colonies, cancer,
+compucell3d: developmental biology, evolution, the immune system, tissue
+compucell3d: engineering, toxicology and even non-cellular soft materials.
+compucell3d: 
+compucell3d: 
+compucell3d: 

xap/compucell3d/twedit++.desktop

@@ -0,0 +1,7 @@
+[Desktop Entry]
+Name=Twedit++
+Comment=Cell modeling environment editor
+Type=Application
+Categories=Education;Science;
+Exec=/usr/bin/twedit++
+Terminal=false

xap/compucell3d/twedit++.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+exec /opt/compucell3d/twedit++.sh $@