{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/322","labels_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/322/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/322/comments","events_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/322/events","html_url":"https://github.com/choderalab/openpathsampling/pull/322","id":110327666,"number":322,"title":"Clean up ipynb tests","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},"labels":[],"state":"closed","locked":false,"assignee":{"login":"jhprinz","id":5091934,"avatar_url":"https://avatars.githubusercontent.com/u/5091934?v=3","gravatar_id":"","url":"https://api.github.com/users/jhprinz","html_url":"https://github.com/jhprinz","followers_url":"https://api.github.com/users/jhprinz/followers","following_url":"https://api.github.com/users/jhprinz/following{/other_user}","gists_url":"https://api.github.com/users/jhprinz/gists{/gist_id}","starred_url":"https://api.github.com/users/jhprinz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhprinz/subscriptions","organizations_url":"https://api.github.com/users/jhprinz/orgs","repos_url":"https://api.github.com/users/jhprinz/repos","events_url":"https://api.github.com/users/jhprinz/events{/privacy}","received_events_url":"https://api.github.com/users/jhprinz/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/choderalab/openpathsampling/milestones/1","html_url":"https://github.com/choderalab/openpathsampling/milestones/1.0","labels_url":"https://api.github.com/repos/choderalab/openpathsampling/milestones/1/labels","id":882847,"number":1,"title":"1.0","description":"Issues 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":8,"closed_issues":33,"state":"open","created_at":"2014-11-27T17:27:40Z","updated_at":"2015-10-15T09:11:00Z","due_on":null,"closed_at":null},"comments":7,"created_at":"2015-10-07T22:03:48Z","updated_at":"2015-10-15T12:01:01Z","closed_at":"2015-10-15T09:11:00Z","pull_request":{"url":"https://api.github.com/repos/choderalab/openpathsampling/pulls/322","html_url":"https://github.com/choderalab/openpathsampling/pull/322","diff_url":"https://github.com/choderalab/openpathsampling/pull/322.diff","patch_url":"https://github.com/choderalab/openpathsampling/pull/322.patch"},"body":"Lately, tests have been failing due to Travis’s 50-minute time constraint. Some of this might be fixed by changing the caching behavior as done in #300, but even so, our integration tests include redundancies which should be removed.\r\n\r\nMost obvious redundancy: we call `sliced_sequential` twice. That’s just silly. In fact, I don’t think we need to run that one at all. If we need a check on that, it should really be in the nosetests: that notebook was intended for documentation, not testing.\r\n\r\nThe same is true of the `langevin_integrator` notebook. That was me (1) using visual inspection of distributions to check that the integrator was working correctly; and (2) learning how to use IPython notebooks and matplotlib. That test doesn’t actually test anything extra unless you visually inspect the results. I’ll remove it from the tests.\r\n\r\nFinally, we have the `toy_bootstrapping`, `toy_tis`, and `toy_analysis` notebooks. Functionally, everything that is done in there can be in the MSTIS and MISTIS examples. We have to run both the MSTIS and MISTIS data-generating runs to test those approaches, but then don’t have to also run the stuff in `toy_tis`. Part of this PR will be ensuring that everything from the toy examples (especially analysis) is also done in the MSTIS example.\r\n\r\n- [x] Remove `sliced_sequential` and `langevin_integrator_check`\r\n- [x] Split `multistate_system_setup.ipynb` into `mstis_bootstrap.ipynb` and `mstis.ipynb`\r\n- [x] Reloading trajectories from mstis_bootstrap in mstis; test `map_trajectory_to_ensembles`, and `translate_ensembles`\r\n- [x] Create `PathSampling.run_until(stepnum)` which runs until the given number of steps are stored\r\n- [x] Use `PathSampling.run_until` for test scripts\r\n- [x] Add move scheme checks to `mstis_analysis`\r\n- [x] Add `PathTree` visualization to `mstis_analysis`\r\n- [x] Add visualization of individual trajectories\r\n- [x] Add path length plot to `mstis_analysis`\r\n- [x] Add crossing probability plots to `mstis_analysis`\r\n- [x] Add direct plotting of max lambda to `mstis_analysis`\r\n- [x] Add TCP result plots to `mstis_analysis`\r\n- [x] Add lists with the fluxes for each state in `mstis_analysis`; CTP for each transition\r\n- [x] Fix `repex_networks.ipynb` to work with new input data\r\n- [x] Remove testing calls of `toy_bootstrapping.ipynb`, `toy_tis.ipynb`, `toy_analysis.ipynb`\r\n- [x] Add text to `mstis_bootstrapping` and `mstis` to explain what is going on\r\n\r\n***\r\n\r\nHighlighting a few specific points:\r\n* `PathSampling.run_until(stepnum)`: We need ~200-300 MC steps for analysis to work. Sometimes it takes more than 10 minutes to run 300 steps. So we have 250, and restart. Then the next run, we get another 250 (for 500 total), and restart -- we could have stopped at 300, but instead we try to get 300 within 10 minutes each time. This new function figures out how much is already in storage, then calls `run` for `stepnum - n_steps_in_storage` steps.\r\n* `mstis_analysis` will be the main analysis showcase, showing all the tricks that were previously in the `toy_analysis` scripts. The MSTIS runs will also show how to do bootstrapping in a separate file from the main run, to illustrate how to load samples from a file. The combination of these facts allow us to remove the toy_bootstrapping, toy_tis, and toy_analysis scripts.\r\n\r\nAlso, I re-ordered the tests a bit so that the things which I think are currently most likely to fail come earlier (mainly, that means I moved `alanine.ipynb` much later in the process, because I think the stuff in there is a lot more stable now than in the mstis/mistis.) If the test is going to fail, we might as well make it fail quickly. The rest of the test notebooks still run, but we as developers can see a problem sooner (if we’re watching Travis).\r\n"},"comment":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/comments/148366125","html_url":"https://github.com/choderalab/openpathsampling/pull/322#issuecomment-148366125","issue_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/322","id":148366125,"user":{"login":"jhprinz","id":5091934,"avatar_url":"https://avatars.githubusercontent.com/u/5091934?v=3","gravatar_id":"","url":"https://api.github.com/users/jhprinz","html_url":"https://github.com/jhprinz","followers_url":"https://api.github.com/users/jhprinz/followers","following_url":"https://api.github.com/users/jhprinz/following{/other_user}","gists_url":"https://api.github.com/users/jhprinz/gists{/gist_id}","starred_url":"https://api.github.com/users/jhprinz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhprinz/subscriptions","organizations_url":"https://api.github.com/users/jhprinz/orgs","repos_url":"https://api.github.com/users/jhprinz/repos","events_url":"https://api.github.com/users/jhprinz/events{/privacy}","received_events_url":"https://api.github.com/users/jhprinz/received_events","type":"User","site_admin":false},"created_at":"2015-10-15T12:01:01Z","updated_at":"2015-10-15T12:01:01Z","body":"Comment on my `run_until` comment: It is a function of a PathSampling and thus forget the complain about engine and storage. But would it be useful to have two numbers like run 100 steps now until a maximum + stored ones is like 300 steps? It seems that now it runs 300 and next time it does run none.\r\nIs that correct?"}}