{"id":202,"date":"2013-04-01T18:40:56","date_gmt":"2013-04-01T18:40:56","guid":{"rendered":"http:\/\/www.reades.com\/?p=202"},"modified":"2013-04-01T18:40:56","modified_gmt":"2013-04-01T18:40:56","slug":"plotting-igraph-on-lion-and-mountain-lion","status":"publish","type":"post","link":"http:\/\/www.reades.com\/wp\/?p=202","title":{"rendered":"Plotting & iGraph on Lion and Mountain Lion"},"content":{"rendered":"

\t\t\t\tNote: this was previously posted at simulacra.info<\/a>, but I am in the process of (re)organising my technical notes and tutorials.<\/i><\/p>\n

After giving up on Gephi (again, I really should learn), I decided it was time to get to grips with Python and iGraph since I really need to produce multiple iterations of a graph. The matmos at CASA have, of course, been touting Python for ages, but I’ve just not had the time\/incentive to install and, more importantly, actually get around to using it… until now. Of course, like all such migrations, there has been a bit of a learning curve, so I’m documenting this to save you (and me) the trouble later because it turns out that Lion and Mountain Lion aren’t 100% iGraph friendly out of the box.<\/p>\n

iGraph itself is easy to install, you can just download and run the installer from\u00a0SourceForge<\/a>\u00a0but the supporting libraries to enable plotting have some issues. Below is what I\u00a0adapted from information provided by the people at \u00a0ffMpeg<\/a>.<\/p>\n

You will need to start by grabbing\u00a0xz<\/a>, which is (yet another) compression\/decompression library promising better performance than the venerable gz or bzip:
\n
\n.\/configure
\nmake && sudo make install
\n<\/code><\/p>\n

You need xz so that you can decompress glib, but before you can compile glib, you will also need the latest version of\u00a0gettext<\/a>. Furthermore,\u00a0per the instructions<\/a>\u00a0you will need to manually edit one of the files to get it to compile on Lion or Mountain Lion. Namely, open:<\/p>\n

gettext-tools\/gnulib-lib\/stpncpy.c<\/pre>\n
and change it such that you have added a line reading:<\/p>\n
#undef stpncpy<\/pre>\n
just before the line reading:<\/p>\n
#ifndef weak_alias<\/pre>\n
From there, it’s your usual:
\n
\n.\/configure
\nmake && sudo make install
\n<\/code><\/p>\n
Now you can finally move on to installing\u00a0glib<\/a>, which will be need for compiling Cairo properly. Note that this is the point where you have to start passing in more and more command line arguments to configure:
\n
\nxz -d glib-2.33.10.tar.xz
\ntar -xvf\u00a0glib-2.33.10.tar
\ncd glib-2.33.10
\nLIBFFI_CFLAGS=-I\/usr\/include\/ffi LIBFFI_LIBS=-lffi .\/configure; make && sudo make\u00a0install
\n<\/code><\/p>\n
Phew, we’re getting there. Now it’s time for\u00a0pkg-config<\/a>:
\n
\nGLIB_CFLAGS=\"-I\/usr\/local\/include\/glib-2.0 -I\/usr\/local\/lib\/glib-2.0\/include\" GLIB_LIBS=\"-lglib-2.0 -lgio-2.0\" .\/configure --with-pc-path=\"\/usr\/X11\/lib\/pkgconfig:\/usr\/X11\/share\/pkgconfig:\/usr\/lib\/pkgconfig:\/usr\/local\/lib\/pkgconfig\"
\nmake && sudo make install
\n<\/code><\/p>\n
I was able to skip straight to installing pycairo because I had already installed Cairo as part of my last update to\u00a0QGIS<\/a>. The excellent\u00a0KyngChaos<\/a>\u00a0has a\u00a0handy set of installers<\/a>\u00a0to keep things simple.<\/p>\n
And finally it’s time for\u00a0pyCairo<\/a>\u00a0(you probably want py2cairo since OSX is using Python 2.7):
\n
\n.\/waf configure
\n.\/waf build
\nsudo .\/waf install<\/code><\/p>\n
You may also care to add this line to your<\/p>\n
.bash_login<\/pre>\n
file:
\n
\nexport PYTHONPATH=\"\/usr\/lib\/python2.7:$PYTHONPATH\"
\n<\/code>
\n(You may also\u00a0not<\/i>\u00a0want to add\u00a0python2.6<\/code>\u00a0or\u00a0python2.5<\/code>\u00a0to your Python path since this will give you some interesting errors… as I discovered.)\t\t<\/p>\n","protected":false},"excerpt":{"rendered":"
Note: this was previously posted at simulacra.info, but I am in the process of (re)organising my technical notes and tutorials. After giving up on Gephi (again, I really should learn), I decided it was time to get to grips with Python and iGraph since I really need to produce multiple iterations of a graph. The […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[12],"tags":[58,74,85,114],"class_list":["post-202","post","type-post","status-publish","format-standard","hentry","category-tutorials","tag-igraph","tag-networks","tag-python","tag-visualisation"],"_links":{"self":[{"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=\/wp\/v2\/posts\/202","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=202"}],"version-history":[{"count":0,"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=\/wp\/v2\/posts\/202\/revisions"}],"wp:attachment":[{"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=202"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=202"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.reades.com\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=202"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}