{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/events","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863","id":157405554,"number":863,"title":"Diffusion Map Refactor/Implementation","user":{"login":"jdetle","id":10944582,"avatar_url":"https://avatars.githubusercontent.com/u/10944582?v=3","gravatar_id":"","url":"https://api.github.com/users/jdetle","html_url":"https://github.com/jdetle","followers_url":"https://api.github.com/users/jdetle/followers","following_url":"https://api.github.com/users/jdetle/following{/other_user}","gists_url":"https://api.github.com/users/jdetle/gists{/gist_id}","starred_url":"https://api.github.com/users/jdetle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdetle/subscriptions","organizations_url":"https://api.github.com/users/jdetle/orgs","repos_url":"https://api.github.com/users/jdetle/repos","events_url":"https://api.github.com/users/jdetle/events{/privacy}","received_events_url":"https://api.github.com/users/jdetle/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Component-Analysis","name":"Component-Analysis","color":"0088ee"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9","html_url":"https://github.com/MDAnalysis/mdanalysis/milestones/0.16.0","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9/labels","id":1716502,"number":9,"title":"0.16.0","description":"","creator":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"open_issues":16,"closed_issues":8,"state":"open","created_at":"2016-04-19T08:42:42Z","updated_at":"2016-06-13T12:21:58Z","due_on":null,"closed_at":null},"comments":32,"created_at":"2016-05-29T20:53:59Z","updated_at":"2016-06-13T23:52:56Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/863","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/863.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/863.patch"},"body":"Fixes #857\r\n\r\nChanges made in this Pull Request:\r\n- Refactor of @euhruska's work to fit bauhaus style\r\n- Currently working through literature to ensure module fits researcher needs, agrees with theory.\r\n\r\nTODO:\r\n---------\r\n- [ ] Write up API for creating epsilon class that takes DistMatrix as an initialization argument, to be used in diffusion maps for epsilon determination.\r\n- [ ] I might be mistaken, but currently it seems like we are only accounting for diffusion time equal to one. If I'm right we need to fix this.\r\n- [ ] Perhaps create a new dimensionreduction module to keep more general objects like covariance matrix and distmatrix that are used in a variety of different dimension reduction techniques. \r\n- [ ] increase tests for different step choices and selections.\r\n\r\nPR Checklist\r\n------------\r\n - [ ] Tests?\r\n - [x] Docs?\r\n - [x] CHANGELOG updated?\r\n - [x] Issue raised/referenced?\r\n"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/225742097","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863#issuecomment-225742097","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863","id":225742097,"user":{"login":"dotsdl","id":1326811,"avatar_url":"https://avatars.githubusercontent.com/u/1326811?v=3","gravatar_id":"","url":"https://api.github.com/users/dotsdl","html_url":"https://github.com/dotsdl","followers_url":"https://api.github.com/users/dotsdl/followers","following_url":"https://api.github.com/users/dotsdl/following{/other_user}","gists_url":"https://api.github.com/users/dotsdl/gists{/gist_id}","starred_url":"https://api.github.com/users/dotsdl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dotsdl/subscriptions","organizations_url":"https://api.github.com/users/dotsdl/orgs","repos_url":"https://api.github.com/users/dotsdl/repos","events_url":"https://api.github.com/users/dotsdl/events{/privacy}","received_events_url":"https://api.github.com/users/dotsdl/received_events","type":"User","site_admin":false},"created_at":"2016-06-13T23:52:56Z","updated_at":"2016-06-13T23:52:56Z","body":"@kain88-de on ``DistMat``, I say just expose the resulting ``distance_matrix`` as a property that points to the result after it's been calculated (*a la* scikit-learn). Since the result is just a ``numpy`` array, we leave it up to the user to store it however they want.\r\n\r\nDoes that help?"}}
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