In almost any up-to-date Linux distribution the dependencies of pypath are built-in, or provided by the distributors. You only need to install a couple of things in your package manager (cairo, py(2)cairo, igraph, python(2)-igraph, graphviz, pygraphviz), and after install pypath by pip (see below). If any module still missing, you can install them the usual way by pip or your package manager.
igraph C library, cairo and pycairo¶
python(2)-igraph is a Python interface to use the igraph C library. The C library must be installed. The same goes for cairo, py(2)cairo and graphviz.
Directly from git¶
pip install git+https://github.com/saezlab/pypath.git
Download the package from /dist, and install with pip:
pip install pypath-x.y.z.tar.gz
Build source distribution¶
Clone the git repo, and run setup.py:
python setup.py sdist
Mac OS X¶
On OS X installation is not straightforward primarily because cairo needs to be compiled from source. We provide 2 scripts here: the mac-install-brew.sh installs everything with HomeBrew, and mac-install-conda.sh installs from Anaconda distribution. With these scripts installation of igraph, cairo and graphviz goes smoothly most of the time, and options are available for omitting the 2 latter. To know more see the description in the script header. There is a third script mac-install-source.sh which compiles everything from source and presumes only Python 2.7 and Xcode installed. We do not recommend this as it is time consuming and troubleshooting requires expertise.
no module named ...when you try to load a module in Python. Did theinstallation of the module run without error? Try to run again the specific part from the mac install shell script to see if any error comes up. Is the path where the module has been installed in your
echo $PYTHONPATHto see the current paths. Add your local install directories if those are not there, e.g.
export PYTHONPATH="/Users/me/local/python2.7/site-packages:$PYTHONPATH". If it works afterwards, don’t forget to append these export path statements to your
~/.bash_profile, so these will be set every time you launch a new shell.
pkgconfignot found. Check if the
$PKG_CONFIG_PATHvariable is set correctly, and pointing on a directory where pkgconfig really can be found.
Error while trying to install py(2)cairo by pip. py(2)cairo could not be installed by pip, but only by waf. Please set the
$PKG_CONFIG_PATHbefore. See mac-install-source.sh on how to install with waf.
Error at pygraphviz build:
graphviz/cgraph.h file not found. This is because the directory of graphviz detected wrong by pkgconfig. See mac-install-source.sh how to set include dirs and library dirs by
Can not install bioservices, because installation of jurko-suds fails. Ok, this fails because pip is not able to install the recent version of setuptools, because a very old version present in the system path. The development version of jurko-suds does not require setuptools, so you can install it directly from git as it is done in mac-install-source.sh.
In Anaconda, pypath can be imported, but the modules and classes are missing. Apparently Anaconda has some built-in stuff called pypath. This has nothing to do with this module. Please be aware that Anaconda installs a completely separated Python distribution, and does not detect modules in the main Python installation. You need to install all modules within Anaconda’s directory. mac-install-conda.sh does exactly this. If you still experience issues, please contact us.
Not many people have used pypath on Microsoft computers so far. Please share your experiences and contact us if you encounter any issue. We appreciate your feedback, and it would be nice to have better support for other computer systems.
The same workflow like you see in
mac-install-conda.sh should work for
Anaconda on Windows. The only problem you certainly will encounter is that not
all the channels have packages for all platforms. If certain channel provides
no package for Windows, or for your Python version, you just need to find an
other one. For this, do a search:
anaconda search -t conda <package name>
For example, if you search for pycairo, you will find out that vgauther
provides it for osx-64, but only for Python 3.4, while richlewis provides
also for Python 3.5. And for win-64 platform, there is the channel of
KristanAmstrong. Go along all the commands in
modify the channel if necessary, until all packages install successfully.
With other Python distributions¶
Here the basic principles are the same as everywhere: first try to install all external dependencies, after pip install should work. On Windows certain packages can not be installed by compiled from source by pip, instead the easiest to install them precompiled. These are in our case fisher, lxml, numpy (mkl version), pycairo, igraph, pygraphviz, scipy and statsmodels. The precompiled packages are available here: http://www.lfd.uci.edu/~gohlke/pythonlibs/. We tested the setup with Python 3.4.3 and Python 2.7.11. The former should just work fine, while with the latter we have issues to be resolved.
“No module fabric available.” – or pysftp missing: this is not
important, only certain data download methods rely on these modules, but likely you won’t call those at all. * Progress indicator floods terminal: sorry about that, will be fixed soon. * Encoding related exceptions in Python2: these might occur at some points in the module, please send the traceback if you encounter one, and we will fix as soon as possible.
Special thanks to Jorge Ferreira for testing pypath on Windows!