{"action":"created","comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/50320657","id":50320657,"diff_hunk":"@@ -584,19 +584,33 @@ def output_exists(self, force=False):\n         \"\"\"\n         return os.path.isfile(self.output) and not (self.force or force)\n \n-    def run(self, store=True, force=False, start_frame=1, end_frame=None, step_value=1):\n+    def run(self, store=True, force=False, start=0, stop=None, step=1, **kwargs):\n         \"\"\"Analyze trajectory and produce timeseries.\n \n         Stores results in :attr:`ContactAnalysis1.timeseries` (if store=True)\n         and writes them to a data file. The average q is written to a second\n         data file.\n-        *start_frame*\n-            The value of the first frame number in the trajectory to be used (default: frame 1)\n-        *end_frame*\n-            The value of the last frame number in the trajectory to be used (default: None -- use all frames)\n-        *step_value*\n+        *start*\n+            The value of the first frame index in the trajectory to be used (default: index 0)\n+        *stop*\n+            The value of the last frame index in the trajectory to be used (default: None -- use all frames)\n+        *step*\n             The number of frames to skip during trajectory iteration (default: use every frame)\n         \"\"\"\n+        import warnings\n+\n+        if 'start_frame' in kwargs:\n+            warnings.warn(\"start_frame argument has been deprecated, use start instead\")","path":"package/MDAnalysis/analysis/contacts.py","position":26,"original_position":26,"commit_id":"22027d0679fd6675c6f48df62d7e35a923ecb947","original_commit_id":"22027d0679fd6675c6f48df62d7e35a923ecb947","user":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"body":"I nevertheless think that these should be `DeprecationWarning`, just because it's the right semantics.","created_at":"2016-01-20T21:19:15Z","updated_at":"2016-01-20T21:19:15Z","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/638#discussion_r50320657","pull_request_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/638","_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/50320657"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/638#discussion_r50320657"},"pull_request":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/638"}}},"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/638","id":56490314,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/638","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/638.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/638.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/638","number":638,"state":"open","locked":false,"title":"Issue 624 -- ContactAnalysis1","user":{"login":"tylerjereddy","id":7903078,"avatar_url":"https://avatars.githubusercontent.com/u/7903078?v=3","gravatar_id":"","url":"https://api.github.com/users/tylerjereddy","html_url":"https://github.com/tylerjereddy","followers_url":"https://api.github.com/users/tylerjereddy/followers","following_url":"https://api.github.com/users/tylerjereddy/following{/other_user}","gists_url":"https://api.github.com/users/tylerjereddy/gists{/gist_id}","starred_url":"https://api.github.com/users/tylerjereddy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tylerjereddy/subscriptions","organizations_url":"https://api.github.com/users/tylerjereddy/orgs","repos_url":"https://api.github.com/users/tylerjereddy/repos","events_url":"https://api.github.com/users/tylerjereddy/events{/privacy}","received_events_url":"https://api.github.com/users/tylerjereddy/received_events","type":"User","site_admin":false},"body":"Resolves #624 by setting the default `start_frame` for the `ContactAnalysis1` `run()` method to 0, and updates the docstring as well. A simple unit test was also included. Note that a new testing module was created for the latter (it seems this analysis module wasn't covered at all--or at least any tests haven't been placed in a dedicated testing module like many of the other analysis modules have). \r\n\r\nAt first, one might suspect that this bug is the result of the `0.10` to `0.11` 0-based frame numbering change. But even when frame numbering was 1 based, indexing a trajectory from 1 (the default) would start at the second frame, so it was still wrong to use a default `start_frame` of 1.\r\n\r\nOne could probably argue that we should change `start_frame` to `start_index`, since it really is the trajectory index. I did not make this adjustment, perhaps because frame and index number are now unified in the 0-based system. 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