{"action":"created","issue":{"url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/32","repository_url":"https://api.github.com/repos/kundajelab/tfmodisco","labels_url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/32/comments","events_url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/32/events","html_url":"https://github.com/kundajelab/tfmodisco/issues/32","id":371565931,"node_id":"MDU6SXNzdWUzNzE1NjU5MzE=","number":32,"title":"Support for win32","user":{"login":"TommyJW","id":28304660,"node_id":"MDQ6VXNlcjI4MzA0NjYw","avatar_url":"https://avatars0.githubusercontent.com/u/28304660?v=4","gravatar_id":"","url":"https://api.github.com/users/TommyJW","html_url":"https://github.com/TommyJW","followers_url":"https://api.github.com/users/TommyJW/followers","following_url":"https://api.github.com/users/TommyJW/following{/other_user}","gists_url":"https://api.github.com/users/TommyJW/gists{/gist_id}","starred_url":"https://api.github.com/users/TommyJW/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TommyJW/subscriptions","organizations_url":"https://api.github.com/users/TommyJW/orgs","repos_url":"https://api.github.com/users/TommyJW/repos","events_url":"https://api.github.com/users/TommyJW/events{/privacy}","received_events_url":"https://api.github.com/users/TommyJW/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-10-18T14:43:27Z","updated_at":"2018-10-18T17:04:12Z","closed_at":null,"author_association":"NONE","body":"Looks like the dependency modisco/cluster/phenograph/core.py uses an old codebase:\r\n\r\n#copied from https://github.com/jacoblevine/PhenoGraph/blob/master/phenograph/core.py\r\n\r\nThe most recent update from that repo includes support for win32 systems.\r\n\r\nI did try to modify a local copy of:\r\nmodisco/cluster/core.py  -- edit, not sure this file was modified, not near system right now\r\nmodisco/cluster/__init__.py\r\nmodisco/affinitymat/transformers.py\r\n\r\nto import a copy of jacoblevine/phenograph installed from pip instead (for the up to date copy) but the sample TF MoDISco TAL GATA breaks due to other functions missing from the phenograph .py's\r\n\r\nCould we update modisco to require jacoblevine/phenograph as a dependency and add hooks or overrides instead of extending the .pys directly through copy/paste?\r\n\r\nAlternatively is there a known list of all functions that were added to pheonograph's files that I could use to build this?"},"comment":{"url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/comments/431087063","html_url":"https://github.com/kundajelab/tfmodisco/issues/32#issuecomment-431087063","issue_url":"https://api.github.com/repos/kundajelab/tfmodisco/issues/32","id":431087063,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMTA4NzA2Mw==","user":{"login":"AvantiShri","id":2302598,"node_id":"MDQ6VXNlcjIzMDI1OTg=","avatar_url":"https://avatars2.githubusercontent.com/u/2302598?v=4","gravatar_id":"","url":"https://api.github.com/users/AvantiShri","html_url":"https://github.com/AvantiShri","followers_url":"https://api.github.com/users/AvantiShri/followers","following_url":"https://api.github.com/users/AvantiShri/following{/other_user}","gists_url":"https://api.github.com/users/AvantiShri/gists{/gist_id}","starred_url":"https://api.github.com/users/AvantiShri/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AvantiShri/subscriptions","organizations_url":"https://api.github.com/users/AvantiShri/orgs","repos_url":"https://api.github.com/users/AvantiShri/repos","events_url":"https://api.github.com/users/AvantiShri/events{/privacy}","received_events_url":"https://api.github.com/users/AvantiShri/received_events","type":"User","site_admin":false},"created_at":"2018-10-18T17:04:12Z","updated_at":"2018-10-18T17:04:12Z","author_association":"COLLABORATOR","body":"Oof, it’s actually more complex than that; I had to modify the Louvain community detection binaries for tfmodisco. Phenograph ships precompiled binaries, but I was only able to prepare a precompiled binary for osx and linux because I literally don’t have access to a windows system. I can look into modifying setup.py to compile things on the fly. Part of the problem is that there are 3 binaries, two of which I modified, and 1 of which was modified by the author of phenograph - but the author of phenograph has not released the source code for those modifications (despite multiple requests https://github.com/jacoblevine/PhenoGraph/issues/9), which is why I was relying on shipping the precompiled binaries rather than having the user compile from source.\r\n\r\nIn the meantime, are you able to compile the code here from source: https://github.com/kundajelab/modisco_louvain? If so you could just update your version of tfmodisco to have the precompiled windows binaries."}}
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