{"action":"created","comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/43705477","id":43705477,"diff_hunk":"@@ -387,7 +388,7 @@ def open_trajectory(self):\n \n         return self.xyzfile\n \n-    def Writer(self, filename, n_atoms=None, **kwargs):\n+    def Writer(self, filename, atoms=None, **kwargs):","path":"package/MDAnalysis/coordinates/XYZ.py","position":13,"original_position":13,"commit_id":"31f260ac96c252b3b44b6d6ad90b238f07c0abb1","original_commit_id":"31f260ac96c252b3b44b6d6ad90b238f07c0abb1","user":{"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},"body":"this would bring XYZ out of line with all the other Writers, so it's probably best to leave this as `n_atoms`","created_at":"2015-11-03T00:55:24Z","updated_at":"2015-11-03T00:55:24Z","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/515#discussion_r43705477","pull_request_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515","_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/43705477"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/515#discussion_r43705477"},"pull_request":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515"}}},"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515","id":49502391,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/515","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/515.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/515.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/515","number":515,"state":"open","locked":false,"title":"Natoms kwarg","user":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars.githubusercontent.com/u/4302678?v=3","gravatar_id":"","url":"https://api.github.com/users/kain88-de","html_url":"https://github.com/kain88-de","followers_url":"https://api.github.com/users/kain88-de/followers","following_url":"https://api.github.com/users/kain88-de/following{/other_user}","gists_url":"https://api.github.com/users/kain88-de/gists{/gist_id}","starred_url":"https://api.github.com/users/kain88-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kain88-de/subscriptions","organizations_url":"https://api.github.com/users/kain88-de/orgs","repos_url":"https://api.github.com/users/kain88-de/repos","events_url":"https://api.github.com/users/kain88-de/events{/privacy}","received_events_url":"https://api.github.com/users/kain88-de/received_events","type":"User","site_admin":false},"body":"This tests that all writer accept an n_atoms kwarg. Only special container formats that can write a different model for each frame (PDB, XYZ) don't need that argument.  I also added the option that XYZReader.Writer now accepts a general `atoms` argument that can be either an integer or an AtomGroup.  (btw all Readers that we port to the new tests will have to follow that API)\r\n\r\nSee #511 for discussions","created_at":"2015-11-02T23:41:49Z","updated_at":"2015-11-03T00:55:24Z","closed_at":null,"merged_at":null,"merge_commit_sha":"02b806a08a59a5788be3ce30a3b9b4e0e5f07f22","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515/commits","review_comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515/comments","review_comment_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments{/number}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/515/comments","statuses_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/statuses/31f260ac96c252b3b44b6d6ad90b238f07c0abb1","head":{"label":"kain88-de:natoms-kwarg","ref":"natoms-kwarg","sha":"31f260ac96c252b3b44b6d6ad90b238f07c0abb1","user":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars.githubusercontent.com/u/4302678?v=3","gravatar_id":"","url":"https://api.github.com/users/kain88-de","html_url":"https://github.com/kain88-de","followers_url":"https://api.github.com/users/kain88-de/followers","following_url":"https://api.github.com/users/kain88-de/following{/other_user}","gists_url":"https://api.github.com/users/kain88-de/gists{/gist_id}","starred_url":"https://api.github.com/users/kain88-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kain88-de/subscriptions","organizations_url":"https://api.github.com/users/kain88-de/orgs","repos_url":"https://api.github.com/users/kain88-de/repos","events_url":"https://api.github.com/users/kain88-de/events{/privacy}","received_events_url":"https://api.github.com/users/kain88-de/received_events","type":"User","site_admin":false},"repo":{"id":40093220,"name":"mdanalysis","full_name":"kain88-de/mdanalysis","owner":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars.githubusercontent.com/u/4302678?v=3","gravatar_id":"","url":"https://api.github.com/users/kain88-de","html_url":"https://github.com/kain88-de","followers_url":"https://api.github.com/users/kain88-de/followers","following_url":"https://api.github.com/users/kain88-de/following{/other_user}","gists_url":"https://api.github.com/users/kain88-de/gists{/gist_id}","starred_url":"https://api.github.com/users/kain88-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kain88-de/subscriptions","organizations_url":"https://api.github.com/users/kain88-de/orgs","repos_url":"https://api.github.com/users/kain88-de/repos","events_url":"https://api.github.com/users/kain88-de/events{/privacy}","received_events_url":"https://api.github.com/users/kain88-de/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/kain88-de/mdanalysis","description":"MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories.","fork":true,"url":"https://api.github.com/repos/kain88-de/mdanalysis","forks_url":"https://api.github.com/repos/kain88-de/mdanalysis/forks","keys_url":"https://api.github.com/repos/kain88-de/mdanalysis/keys{/key_id}","collaborators_url":"https://api.github.com/repos/kain88-de/mdanalysis/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/kain88-de/mdanalysis/teams","hooks_url":"https://api.github.com/repos/kain88-de/mdanalysis/hooks","issue_events_url":"https://api.github.com/repos/kain88-de/mdanalysis/issues/events{/number}","events_url":"https://api.github.com/repos/kain88-de/mdanalysis/events","assignees_url":"https://api.github.com/repos/kain88-de/mdanalysis/assignees{/user}","branches_url":"https://api.github.com/repos/kain88-de/mdanalysis/branches{/branch}","tags_url":"https://api.github.com/repos/kain88-de/mdanalysis/tags","blobs_url":"https://api.github.com/repos/kain88-de/mdanalysis/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/kain88-de/mdanalysis/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/kain88-de/mdanalysis/git/refs{/sha}","trees_url":"https://api.github.com/repos/kain88-de/mdanalysis/git/trees{/sha}","statuses_url":"https://api.github.com/repos/kain88-de/mdanalysis/statuses/{sha}","languages_url":"https://api.github.com/repos/kain88-de/mdanalysis/languages","stargazers_url":"https://api.github.com/repos/kain88-de/mdanalysis/stargazers","contributors_url":"https://api.github.com/repos/kain88-de/mdanalysis/contributors","subscribers_url":"https://api.github.com/repos/kain88-de/mdanalysis/subscribers","subscription_url":"https://api.github.com/repos/kain88-de/mdanalysis/subscription","commits_url":"https://api.github.com/repos/kain88-de/mdanalysis/commits{/sha}","git_commits_url":"https://api.github.com/repos/kain88-de/mdanalysis/git/commits{/sha}","comments_url":"https://api.github.com/repos/kain88-de/mdanalysis/comments{/number}","issue_comment_url":"https://api.github.com/repos/kain88-de/mdanalysis/issues/comments{/number}","contents_url":"https://api.github.com/repos/kain88-de/mdanalysis/contents/{+path}","compare_url":"https://api.github.com/repos/kain88-de/mdanalysis/compare/{base}...{head}","merges_url":"https://api.github.com/repos/kain88-de/mdanalysis/merges","archive_url":"https://api.github.com/repos/kain88-de/mdanalysis/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/kain88-de/mdanalysis/downloads","issues_url":"https://api.github.com/repos/kain88-de/mdanalysis/issues{/number}","pulls_url":"https://api.github.com/repos/kain88-de/mdanalysis/pulls{/number}","milestones_url":"https://api.github.com/repos/kain88-de/mdanalysis/milestones{/number}","notifications_url":"https://api.github.com/repos/kain88-de/mdanalysis/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/kain88-de/mdanalysis/labels{/name}","releases_url":"https://api.github.com/repos/kain88-de/mdanalysis/releases{/id}","created_at":"2015-08-02T21:22:09Z","updated_at":"2015-08-02T21:22:15Z","pushed_at":"2015-11-02T23:40:11Z","git_url":"git://github.com/kain88-de/mdanalysis.git","ssh_url":"git@github.com:kain88-de/mdanalysis.git","clone_url":"https://github.com/kain88-de/mdanalysis.git","svn_url":"https://github.com/kain88-de/mdanalysis","homepage":"http://www.mdanalysis.org","size":163004,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":false,"has_wiki":true,"has_pages":true,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"develop"}},"base":{"label":"MDAnalysis:develop","ref":"develop","sha":"aac24f9b0faa61ae085d4cc858b13a39d940d861","user":{"login":"MDAnalysis","id":11445951,"avatar_url":"https://avatars.githubusercontent.com/u/11445951?v=3","gravatar_id":"","url":"https://api.github.com/users/MDAnalysis","html_url":"https://github.com/MDAnalysis","followers_url":"https://api.github.com/users/MDAnalysis/followers","following_url":"https://api.github.com/users/MDAnalysis/following{/other_user}","gists_url":"https://api.github.com/users/MDAnalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/MDAnalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MDAnalysis/subscriptions","organizations_url":"https://api.github.com/users/MDAnalysis/orgs","repos_url":"https://api.github.com/users/MDAnalysis/repos","events_url":"https://api.github.com/users/MDAnalysis/events{/privacy}","received_events_url":"https://api.github.com/users/MDAnalysis/received_events","type":"Organization","site_admin":false},"repo":{"id":33389183,"name":"mdanalysis","full_name":"MDAnalysis/mdanalysis","owner":{"login":"MDAnalysis","id":11445951,"avatar_url":"https://avatars.githubusercontent.com/u/11445951?v=3","gravatar_id":"","url":"https://api.github.com/users/MDAnalysis","html_url":"https://github.com/MDAnalysis","followers_url":"https://api.github.com/users/MDAnalysis/followers","following_url":"https://api.github.com/users/MDAnalysis/following{/other_user}","gists_url":"https://api.github.com/users/MDAnalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/MDAnalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MDAnalysis/subscriptions","organizations_url":"https://api.github.com/users/MDAnalysis/orgs","repos_url":"https://api.github.com/users/MDAnalysis/repos","events_url":"https://api.github.com/users/MDAnalysis/events{/privacy}","received_events_url":"https://api.github.com/users/MDAnalysis/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/MDAnalysis/mdanalysis","description":"MDAnalysis is a Python library to analyze molecular dynamics trajectories.","fork":false,"url":"https://api.github.com/repos/MDAnalysis/mdanalysis","forks_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/forks","keys_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/keys{/key_id}","collaborators_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/teams","hooks_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/hooks","issue_events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/events{/number}","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/events","assignees_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/assignees{/user}","branches_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/branches{/branch}","tags_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/tags","blobs_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/git/refs{/sha}","trees_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/git/trees{/sha}","statuses_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/statuses/{sha}","languages_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/languages","stargazers_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/stargazers","contributors_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/contributors","subscribers_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/subscribers","subscription_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/subscription","commits_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/commits{/sha}","git_commits_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/git/commits{/sha}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/comments{/number}","issue_comment_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments{/number}","contents_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/contents/{+path}","compare_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/compare/{base}...{head}","merges_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/merges","archive_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/downloads","issues_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues{/number}","pulls_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls{/number}","milestones_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones{/number}","notifications_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels{/name}","releases_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/releases{/id}","created_at":"2015-04-04T00:39:41Z","updated_at":"2015-10-30T07:11:46Z","pushed_at":"2015-11-02T23:41:49Z","git_url":"git://github.com/MDAnalysis/mdanalysis.git","ssh_url":"git@github.com:MDAnalysis/mdanalysis.git","clone_url":"https://github.com/MDAnalysis/mdanalysis.git","svn_url":"https://github.com/MDAnalysis/mdanalysis","homepage":"http://www.mdanalysis.org","size":199049,"stargazers_count":41,"watchers_count":41,"language":"Python","has_issues":true,"has_downloads":false,"has_wiki":true,"has_pages":true,"forks_count":20,"mirror_url":null,"open_issues_count":64,"forks":20,"open_issues":64,"watchers":41,"default_branch":"develop"}},"_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/515"},"issue":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/515"},"comments":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/515/comments"},"review_comments":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515/comments"},"review_comment":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/515/commits"},"statuses":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/statuses/31f260ac96c252b3b44b6d6ad90b238f07c0abb1"}}}}