{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/1553","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/1553/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/1553/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/1553/events","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/1553","id":244949638,"number":1553,"title":"ENH: Added basic asv benchmark suite to MDAnalysis","user":{"login":"tylerjereddy","id":7903078,"avatar_url":"https://avatars0.githubusercontent.com/u/7903078?v=4","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},"labels":[{"id":195620938,"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/performance","name":"performance","color":"f7c6c7","default":false},{"id":215565587,"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/testing","name":"testing","color":"000000","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":22,"created_at":"2017-07-24T01:04:56Z","updated_at":"2017-08-01T17:34:08Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/1553","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/1553","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/1553.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/1553.patch"},"body":"This feature branch allows `asv` benchmarks to run for the MDAnalysis project with no modification to the location of our `setup.py` (yay !!).\r\n\r\nA minimal set of enabling modifications (to handle `setup.py` in a subdirectory instead of expected project root) in a branch of our fork of `asv` can be seen in the [PR to asv itself](https://github.com/spacetelescope/asv/pull/535). For the near term, I suspect we'll be using our custom fork of `asv`, but longer term I think there are definitely prospects to generalize for `asv` itself so we don't have to maintain the fork indefinitely.\r\n\r\nThis PR supersedes #1399.\r\n\r\nHere is an example of MDAnalysis being benchmarked with our fork of asv (execute from the `benchmarks` folder):\r\n`asv continuous --bench GROReadBench d76c9348 e0bc303 -e`\r\n\r\nOutput (scroll right for bench times):\r\n```\r\n· Creating environments\r\n· Discovering benchmarks\r\n·· Uninstalling from conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six..\r\n·· Installing into conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six..\r\n· Running 2 total benchmarks (2 commits * 1 environments * 1 benchmarks)\r\n[  0.00%] · For mdanalysis commit hash e0bc3034:\r\n[  0.00%] ·· Building for conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six....\r\n[  0.00%] ·· Benchmarking conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six\r\n[ 50.00%] ··· Running GRO.GROReadBench.time_read_GRO_file                                                                                                                                                                            156±0ms\r\n[ 50.00%] · For mdanalysis commit hash d76c9348:\r\n[ 50.00%] ·· Building for conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six....\r\n[ 50.00%] ·· Benchmarking conda-py2.7-Cython-mock-nose-numpy-psutil-pytest-scipy-six\r\n[100.00%] ··· Running GRO.GROReadBench.time_read_GRO_file                                                                                                                                                                            156±0ms\r\nBENCHMARKS NOT SIGNIFICANTLY CHANGED.\r\n```\r\n\r\nAs expected, GRO file reading performance did not change between those two recent commit hashes that didn't touch gro file reading. Of course, far more powerful commands are also possible, and since this solution doesn't relocate `setup.py` I'll see if I can find time to run a nice retroactive analysis of performance this evening. \r\n\r\nI encourage those reviewing this PR to try this out as well.  `asv` commands are [documented online](http://asv.readthedocs.io/en/latest/commands.html).  Don't forget to build `asv` from source using our fork / branch named `flexible_build`."},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/319441379","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/1553#issuecomment-319441379","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/1553","id":319441379,"user":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars0.githubusercontent.com/u/4302678?v=4","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},"created_at":"2017-08-01T17:34:08Z","updated_at":"2017-08-01T17:34:08Z","body":"Anaconda.org blocked Travis in the last day. This has been fixed about 2-3 hours ago"}}
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