{"action":"created","issue":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/386","repository_url":"https://api.github.com/repos/openpathsampling/openpathsampling","labels_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/386/labels{/name}","comments_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/386/comments","events_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/386/events","html_url":"https://github.com/openpathsampling/openpathsampling/pull/386","id":117666374,"number":386,"title":"[WIP] Poor 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that should be solved before first public release.","creator":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":83,"state":"open","created_at":"2014-11-27T17:27:40Z","updated_at":"2016-08-01T20:41:06Z","due_on":null,"closed_at":null},"comments":5,"created_at":"2015-11-18T19:48:04Z","updated_at":"2016-08-02T13:28:31Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/pulls/386","html_url":"https://github.com/openpathsampling/openpathsampling/pull/386","diff_url":"https://github.com/openpathsampling/openpathsampling/pull/386.diff","patch_url":"https://github.com/openpathsampling/openpathsampling/pull/386.patch"},"body":"It isn’t the pretty version that I’d like to have, but I think it will work. Approach described in https://github.com/choderalab/openpathsampling/issues/349#issuecomment-156745744 (and other comments, esp from @bolhuis, in that thread). My opinion on this approach, as I expressed it previously: \"It definitely fell out of the ugly tree, but at least it didn’t hit every branch on the way down.\"\r\n\r\n- [x] PoorSingleReplicaStrategy\r\n- [x] Tests for PoorSingleReplicaStrategy\r\n- [x] Add the ability to use the `real_choice_probability` for estimating number of moves\r\n- [x] SRTISMoveScheme (for now, using PoorSRStrat)\r\n- [x] Test notebook for SRTISMoveScheme\r\n- [x] Add support for bias to `EnsembleHop`\r\n- [x] Test that biased ensemble hopping works\r\n- [ ] Analysis for SRTIS scheme\r\n\r\nFuture versions of the SRTISMoveScheme will switch to the better approach, once we have it. But I think this will work in the short term.\r\n\r\n`choice_probability` is still preserved, but is no longer the correct way to estimate the number of total steps needed to get a certain number of trials in a certain mover -- now that will require another thing called `real_choice_probability` which gives the result (assuming equal sampling of each ensemble).\r\n\r\nI'm still not sure that everything in this is safe for all possible move strategies, but it should give us something that is temporarily workable."},"comment":{"url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/comments/236903752","html_url":"https://github.com/openpathsampling/openpathsampling/pull/386#issuecomment-236903752","issue_url":"https://api.github.com/repos/openpathsampling/openpathsampling/issues/386","id":236903752,"user":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"created_at":"2016-08-02T13:28:31Z","updated_at":"2016-08-02T13:28:31Z","body":"This is ready for review as a partially-complete PR. It affects some file-related stuff (initialization/storage of `MoveScheme`), so better to merge it sooner than later.\r\n\r\nAfter this is merged, I'll open a new PR to complete the goals of this one (see #260). It is pretty close."}}
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