8 changed files with 206 additions and 0 deletions
@ -0,0 +1,28 @@
|
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diff -Naur CompuCell3D-20180916.orig/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp CompuCell3D-20180916/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp
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--- CompuCell3D-20180916.orig/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp 2018-07-23 01:30:09.000000000 +0100
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+++ CompuCell3D-20180916/CompuCell3D/core/pyinterface/SerializerDE/SerializerDE.cpp 2018-09-16 17:02:36.870316092 +0100
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@@ -655,7 +655,7 @@
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for(pt.y =0 ; pt.y<fieldDim.y ; ++pt.y)
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for(pt.x =0 ; pt.x<fieldDim.x ; ++pt.x){
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- fieldArray->GetTupleValue(offset,tuple);
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+ fieldArray->GetTypedTuple(offset,tuple);
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// (*fieldPtr)[pt.x][pt.y][pt.z]=Coordinates3D<float>(tuple[0],tuple[1],tuple[2]) ;
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@@ -789,7 +789,7 @@
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if(mitr!=fieldPtr->end()){
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;
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}else{
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- fieldArray->GetTupleValue(offset,tuple);
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+ fieldArray->GetTypedTuple(offset,tuple);
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cerr<<"inserting "<<Coordinates3D<float>(tuple[0],tuple[1],tuple[2])<<endl;
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fieldPtr->insert(make_pair(cell,Coordinates3D<float>(tuple[0],tuple[1],tuple[2])));
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@@ -801,4 +801,4 @@
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fieldDataReader->Delete();
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return true;
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-}
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\ No newline at end of file
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+}
|
@ -0,0 +1,144 @@
|
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#!/bin/bash |
||||
# Build script for Slackware |
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# Copyright (C) 2018 Damien Goutte-Gattat |
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# |
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# Redistribution and use of this script, with or without modifications, |
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# is permitted provided that the following conditions are met: |
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# |
||||
# 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. |
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# |
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# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org> |
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# |
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# Latest CompuCell3D sourcecode is available at: |
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# <http://www.compucell3d.org/>. |
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# |
||||
# Depends: l/PyQt5, l/vtk, l/pyqtgraph, l/qscintilla |
||||
|
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# 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/')} |
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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!" |
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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 |
@ -0,0 +1,7 @@
|
||||
[Desktop Entry] |
||||
Name=CompuCell3D |
||||
Comment=Cell modeling environment |
||||
Type=Application |
||||
Categories=Education;Science; |
||||
Exec=/usr/bin/compucell3d |
||||
Terminal=false |
@ -0,0 +1,2 @@
|
||||
#!/bin/sh |
||||
exec /opt/compucell3d/compucell3d.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 |
@ -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: |
@ -0,0 +1,7 @@
|
||||
[Desktop Entry] |
||||
Name=Twedit++ |
||||
Comment=Cell modeling environment editor |
||||
Type=Application |
||||
Categories=Education;Science; |
||||
Exec=/usr/bin/twedit++ |
||||
Terminal=false |
Loading…
Reference in new issue