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Installation on a Mac OS X Table of Contents • Installation on a Mac OS X Installation notes MacPorts Homebrew Which one ? Installation using MacPort Installation on Mac OS X 10.10 Yosemite Installation on Mac OS X 10.9 Mavericks Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Installation using Homebrew Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Installation on Mac OS X 10.6 Snow Leopard Installation on older Mac OS X Version Uninstalling OpenAlea Note for developpers Note for Python Scientists Installation on a Mac OS X edit 1426868450 [Installation on a Mac OSsection X] 1-40 1/15 documentation:user:installation_mac Edit Installation notes OpenAlea installation is done in two steps. install all dependencies required by OpenAlea as described in this page once dependencies installed, install OpenAlea as described in Building and Installing OpenAlea To install dependencies on Mac OS X, openalea can rely on two package managers, namely Homebrew and Macports. MacPorts MacPorts is a standard Mac OS X tool to facilitate the process of installation of 3rd party programs and libraries. Please follow the instructions on MacPorts webpage to correctly install and setup MacPort installation. Using MacPorts facilitates the process of installation of Openalea dependencies. Please be patient during the process, since some packages have to be compiled by MacPorts. Install MacPorts To install OpenAlea dependencies with Macports, please have a look to section corresponding to your Mac OS X version (see for instance 10.9) MacPorts is recommend system. Documentation for homebrew is not officialy maintained and so can be outdated Homebrew Homebrew is a package management system that simplifies the installation of software on the Mac OS X operating system. It is a free/open source software project to simplify installation of other free/open source software. It is similar in aim and function to MacPorts and Fink (ref: wikipedia) For the installation, follow these 3 steps: Uninstall MacPorts if exists Install Homebrew To install OpenAlea dependencies with Homebrew, please have a look to section corresponding to your Mac OS X version (see for instance 10.9) Which one ? Using MacPorts or Homebrew for Openalea installation is not required, but strongly recommended. Both can be used, so choose the one you prefer but use only one ! 2/15 edit 1426868450 [Installation notes] section 41-2336 documentation:user:installation_mac Edit Installation using MacPort Installation on Mac OS X 10.10 Yosemite Because Mac OS X 10.10 is very young, these instructions will certainly change. See installation for Mac OS X 10.9. Main changes is the renaming of the py27-pil module in py27-Pillow by MacPort. 3/15 sudo port install py27-Pillow Installation on Mac OS X 10.9 Mavericks Openalea works well on OS X 10.9 but several VPlant packages are not yet available. We are working on it to provide full support as soon as possible. Click to display ? Click to hide ? Click to hide ? If macport can't install py27-PyQGLViewer, install pyqglviewer from sources. First download http://gforge.inria.fr/frs/download.php/file/34636/PyQGLViewer-0.13.tgz Then unzip the file. In the repertory PyQGLViewer: python configure.py make [ sudo ] make install Install OpenAlea from sources If it is not done automatically, update the PATH export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/ 2.7 /bin:$PATH In OpenAlea and VPlants source directory, if exists, rename options_macports.py to options.py. If you work on image processing, you should install these libraries sudo port install tiff # pylibtiff to read/write tiff images svn checkout https://pylibtiff.googlecode.com/svn/trunk/ pylibtiff-read-only cd pylibtiff-read-only python setup.py install cd - # pyLSM to read lsm files easy_install pylsm # Scikit-learn sudo port install py-scikit-learn # Vtk only 4/15 sudo port install vtk5 +python27 +qt4_mac An upgrade of macport can cause a segmentation fault at the execution of openalealab and lpy, probably because boost has been compiled with a different compiler. To ensure that the same compiler is used everywhere, compile boost from sources (macport with -s option) and recompile both vplants and openalea: sudo port -s install boost Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Click to display ? Click to hide ? Click to hide ? Install OpenAlea from sources Update the PATH export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/ 2.7 /bin:$PATH edit 1426868450 [Installation using MacPort]section 2337-6651 5/15 documentation:user:installation_mac Edit Installation using Homebrew Click to display ? Click to hide ? Click to hide ? Update your paths to be able to run programs installed from Homebrew directly. Copy/paste this line at the end of your ~/.profile or ~/.bash_profile if it exists. export PATH=/usr/local/bin:$PATH Install Python : # set up some taps and update brew brew tap homebrew/science # a lot of cool formulae for scientific tools brew tap homebrew/python # numpy, scipy brew update && brew upgrade # install a brewed python brew install python pip install --upgrade setuptools pip install --upgrade pip brew linkapps Install dependencies # Install Qt and PyQt brew install qt --with-d-bus --with-qt3support brew install sip pyqt # install PIL, imagemagick, graphviz and other # image generating stuff (qt is nice for viewing) brew install imagemagick graphviz brew install freetype ln -s /usr/local/include/freetype2 /usr/local/include/freetype brew install pillow brew install matplotlib # Useful python libraries pip install nose sphinx pyparsing dateutils pip install python-dateutil 6/15 #install scipy and numpy : brew install scipy # Ann brew install https://raw.github.com/gag/homebrew-science/master/ann.rb # ipython and notebook support brew install zmq pip install ipython[all] # OpenAlea Dependencies brew install gnuplot pip install pyopengl pip install scikit-learn # Install Boost.Python brew install boost brew install boost-python brew install homebrew/science/qhull brew install cgal eigen # Install PyQGLViewer brew install qscintilla2 brew install https://raw.github.com/gbaty/homebrew-formula/master/pyqglviewer.rb sudo ln -s "/usr/local/Cellar/libqglviewer/2.5.1/QGLViewer.framework" "/Library/Frameworks/QGLViewer.framework" ln -s /usr/local/Cellar/libqglviewer/2.5.1/QGLViewer.framework /usr/local/ Frameworks/QGLViewer.framework # Bison/Flex brew install bison brew install flex brew install scons If you work on image processing, you should install these libraries brew install libtiff libpng giflib # pylibtiff to read/write tiff images svn checkout https://pylibtiff.googlecode.com/svn/trunk/ pylibtiff-read-only cd pylibtiff-read-only python setup.py install cd - # pyLSM to read lsm files pip install http://launchpad.net/pylsm/trunk/ 0.1 /+download/pylsm-0.1-r34.orig.tar.gz # Scikit-learn pip install scikit-learn # Vtk only brew install vtk --with-qt --with-python --with-pyqt 7/15 All dependencies are now installed. You can now download OpenAlea, Vplant and ALinea sources. Then if downloaded from archives, decompress it. Finally go into source directory. In OpenAlea and VPlants source directory, if exists, rename options_brew_maverick.py to options.py. If you have an error with libJPEG (and/or libTIFF, libPng, libGIF, ?) add to your ~/.profile: IMGLIBS=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ ImageIO.framework/Versions/A/Resources/ export DYLD_INSERT_LIBRARIES=$IMGLIBS /libJPEG.dylib:$IMGLIBS /libTIFF.dylib:$IMGLIBS / libPng.dylib:$IMGLIBS /libGIF.dylib Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Click to display ? Click to hide ? Click to hide ? Update your paths to be able to run programs installed from Homebrew directly. Copy/paste this line at the end of your ~/.profile. export PATH=/usr/local/bin:$PATH export PYTHONPATH=$HOME/local/lib/python2.7/site-packages:/usr/local/lib/ python2.7/site-packages/:$PYTHONPATH Then install Python # set up some taps and update brew brew tap homebrew/science # a lot of cool formulae for scientific tools brew tap homebrew/python # numpy, scipy brew update && brew upgrade # install a brewed python brew install python # Install Qt and PyQt brew install qt --with-qt3support brew install sip pyqt # install PIL, imagemagick, graphviz and other # image generating stuff (qt is nice for viewing) brew install imagemagick graphviz pip install pillow pip install nose sphinx pyparsing dateutils 8/15 # install numpy and scipy # install openblas (otherwise scipy's arpack tests will fail) brew install openblas brew install numpy --with-openblas brew install scipy --with-openblas # If openblas doesn't compile : brew install numpy brew install scipy brew install ann brew install matplotlib # ipython and notebook support brew install zmq pip install ipython[all] # OpenAlea Dependencies brew install gnuplot pip install pyopengl # Install Boost.Python brew install boost --build-from-source #option required for boost/python brew install qhull brew install cgal eigen # Install PyQGLViewer brew install qscintilla2 brew install https://raw.github.com/pradal/homebrew/master/Library/Formula/ libqglviewer.rb brew install https://raw.github.com/pradal/homebrew/master/Library/Formula/ pyqglviewer.rb brew install scons If you have an error with libJPEG (and/or libTIFF, libPng, libGIF, ?) add to your ~/.profile: IMGLIBS=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ Frameworks/ImageIO.framework/Versions/A/Resources/ export DYLD_INSERT_LIBRARIES=$IMGLIBS/libJPEG.dylib:$IMGLIBS/libTIFF.dylib:
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