{"action":"created","issue":{"url":"https://api.github.com/repos/theislab/scanpy/issues/97","repository_url":"https://api.github.com/repos/theislab/scanpy","labels_url":"https://api.github.com/repos/theislab/scanpy/issues/97/labels{/name}","comments_url":"https://api.github.com/repos/theislab/scanpy/issues/97/comments","events_url":"https://api.github.com/repos/theislab/scanpy/issues/97/events","html_url":"https://github.com/theislab/scanpy/issues/97","id":301993800,"number":97,"title":"Investigate if we can do without networkx","user":{"login":"flying-sheep","id":291575,"avatar_url":"https://avatars0.githubusercontent.com/u/291575?v=4","gravatar_id":"","url":"https://api.github.com/users/flying-sheep","html_url":"https://github.com/flying-sheep","followers_url":"https://api.github.com/users/flying-sheep/followers","following_url":"https://api.github.com/users/flying-sheep/following{/other_user}","gists_url":"https://api.github.com/users/flying-sheep/gists{/gist_id}","starred_url":"https://api.github.com/users/flying-sheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flying-sheep/subscriptions","organizations_url":"https://api.github.com/users/flying-sheep/orgs","repos_url":"https://api.github.com/users/flying-sheep/repos","events_url":"https://api.github.com/users/flying-sheep/events{/privacy}","received_events_url":"https://api.github.com/users/flying-sheep/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-03-03T12:18:06Z","updated_at":"2018-03-05T09:49:09Z","closed_at":null,"author_association":"OWNER","body":"AFAIK networkx and python-igraph do the same thing, only that python-igraph is faster.\r\n\r\nWe also need python-igraph anyway for louvain and so on, so maybe it would be good to get rid of networkx.\r\n\r\nDownside: python-igraph and louvain-igraph is currently deliberately an optional dependency since it’s hard to install on windows. People need to build it themselves (A task that even I didn’t manage by now, and I got *many* things to compile!) or use Christoph Grohlke’s unofficial builds ([here](https://www.lfd.uci.edu/~gohlke/pythonlibs/#python-igraph) and [here](https://www.lfd.uci.edu/~gohlke/pythonlibs/#louvain-igraph))"},"comment":{"url":"https://api.github.com/repos/theislab/scanpy/issues/comments/370365130","html_url":"https://github.com/theislab/scanpy/issues/97#issuecomment-370365130","issue_url":"https://api.github.com/repos/theislab/scanpy/issues/97","id":370365130,"user":{"login":"dawe","id":121868,"avatar_url":"https://avatars2.githubusercontent.com/u/121868?v=4","gravatar_id":"","url":"https://api.github.com/users/dawe","html_url":"https://github.com/dawe","followers_url":"https://api.github.com/users/dawe/followers","following_url":"https://api.github.com/users/dawe/following{/other_user}","gists_url":"https://api.github.com/users/dawe/gists{/gist_id}","starred_url":"https://api.github.com/users/dawe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dawe/subscriptions","organizations_url":"https://api.github.com/users/dawe/orgs","repos_url":"https://api.github.com/users/dawe/repos","events_url":"https://api.github.com/users/dawe/events{/privacy}","received_events_url":"https://api.github.com/users/dawe/received_events","type":"User","site_admin":false},"created_at":"2018-03-05T09:49:09Z","updated_at":"2018-03-05T09:49:09Z","author_association":"COLLABORATOR","body":"@flying-sheep [community module](https://perso.crans.org/aynaud/communities/index.html), which builds on networkx, has a more than decent implementation of Louvain's method. Also, NetworkX 2.1 has been improved over its predecessors. Why dropping igraph isn't an option?"}}
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