{"action":"created","comment":{"url":"https://api.github.com/repos/choderalab/yank/pulls/comments/129194913","pull_request_review_id":51940773,"id":129194913,"diff_hunk":"@@ -1159,32 +1224,52 @@ class ReplicaExchange(object):\n     mcmc_moves : MCMCMove or list of MCMCMove, optional\n         The MCMCMove used to propagate the states. If a list of MCMCMoves,\n         they will be assigned to the correspondent thermodynamic state on\n-        creation. If None is provided, Langevin dynamics with 2fm timestep,\n-        5.0/ps collision rate, and 500 steps per iteration will be used.\n-    number_of_iterations : int, optional\n-        The number of iterations to perform (default is 1).\n-    replica_mixing_scheme : 'swap-all', 'swap-neighbors' or 'none'\n+        creation. If None is provided, Langevin dynamics with 2fm timestep, 5.0/ps collision rate,\n+        and 500 steps per iteration will be used.\n+    number_of_iterations : int, Optional, Default: 1\n+        The number of iterations to perform\n+    replica_mixing_scheme : 'swap-all', 'swap-neighbors' or 'none', Default: 'swap-all'\n         The scheme used to swap thermodynamic states between replicas\n-        (default is 'swap-all').\n     online_analysis_interval : None or Int >= 1, optional, default None\n         Choose the interval at which to perform online analysis of the free energy.\n-        After every interval, the simulation will be stopped and the free energy estimated. If the error in the free\n-            energy estimate is at or below online_analysis_target_error, then the simulation will be considered\n-            completed.\n+\n+        After every interval, the simulation will be stopped and the free energy estimated.\n+\n+        If the error in the free energy estimate is at or below online_analysis_target_error, then the simulation will\n+        be considered completed.\n+\n     online_analysis_target_error : float >= 0, optional, default 0.2\n         The target error for the online analysis measured in kT per phase.\n-            Once the free energy is at or below this value, the phase will be considered complete.\n+\n+        Once the free energy is at or below this value, the phase will be considered complete.\n+\n         If online_analysis_interval is None, this option does nothing.\n+\n     online_analysis_minimum_iterations : int >= 0, optional, default 50\n         Set the minimum number of iterations which must pass before online analysis is carried out.\n+\n         Since the initial samples are likley not to yeild a good estimate of free energy, save time and just skip them\n         If online_analysis_interval is None, this does nothing\n \n     Attributes\n     ----------\n+    n_replicas","path":"Yank/repex.py","position":319,"original_position":319,"commit_id":"509b3360a89bdf076a11e8251af1630b9a3818ef","original_commit_id":"509b3360a89bdf076a11e8251af1630b9a3818ef","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars1.githubusercontent.com/u/3656088?v=4","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"body":"Can you document what the attributes mean, and their types?","created_at":"2017-07-25T01:37:23Z","updated_at":"2017-07-25T01:40:07Z","html_url":"https://github.com/choderalab/yank/pull/722#discussion_r129194913","pull_request_url":"https://api.github.com/repos/choderalab/yank/pulls/722","_links":{"self":{"href":"https://api.github.com/repos/choderalab/yank/pulls/comments/129194913"},"html":{"href":"https://github.com/choderalab/yank/pull/722#discussion_r129194913"},"pull_request":{"href":"https://api.github.com/repos/choderalab/yank/pulls/722"}}},"pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/722","id":131360997,"html_url":"https://github.com/choderalab/yank/pull/722","diff_url":"https://github.com/choderalab/yank/pull/722.diff","patch_url":"https://github.com/choderalab/yank/pull/722.patch","issue_url":"https://api.github.com/repos/choderalab/yank/issues/722","number":722,"state":"open","locked":false,"title":"API, Documentation, and Dropdowns (Oh My!)","user":{"login":"Lnaden","id":3809383,"avatar_url":"https://avatars1.githubusercontent.com/u/3809383?v=4","gravatar_id":"","url":"https://api.github.com/users/Lnaden","html_url":"https://github.com/Lnaden","followers_url":"https://api.github.com/users/Lnaden/followers","following_url":"https://api.github.com/users/Lnaden/following{/other_user}","gists_url":"https://api.github.com/users/Lnaden/gists{/gist_id}","starred_url":"https://api.github.com/users/Lnaden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Lnaden/subscriptions","organizations_url":"https://api.github.com/users/Lnaden/orgs","repos_url":"https://api.github.com/users/Lnaden/repos","events_url":"https://api.github.com/users/Lnaden/events{/privacy}","received_events_url":"https://api.github.com/users/Lnaden/received_events","type":"User","site_admin":false},"body":"This PR is the first of a series dedicated to the website. This particular one contains three major parts:\r\n\r\n1. Fully documented the entire public API in docstrings.\r\n2. Automatic documentation generation on the website in the `API Reference` category\r\n3. Collapsable options in all the YAML pages to clean make things easier to read on not sift through a wall of text.\r\n\r\nThe text changes can be reviewed here, but visual changes (including autodoc generation) must be seen by checking out this branch, *installing yank*, then generating the docs yourself. The autodoc feature of Sphinx looks at the currently installed version by import, not what is in the repo itself (if you know how to change that, please comment).\r\n\r\n@andrrizzi Some of the docstrings I added were for code you wrote, so if you could at minimum review those, that would be very helpful. Thanks in 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