{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/1358","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/1358/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/1358/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/1358/events","html_url":"https://github.com/biopython/biopython/pull/1358","id":248466909,"number":1358,"title":"Replace shlex dependency in mmCIF parsing","user":{"login":"jgreener64","id":6620652,"avatar_url":"https://avatars0.githubusercontent.com/u/6620652?v=4","gravatar_id":"","url":"https://api.github.com/users/jgreener64","html_url":"https://github.com/jgreener64","followers_url":"https://api.github.com/users/jgreener64/followers","following_url":"https://api.github.com/users/jgreener64/following{/other_user}","gists_url":"https://api.github.com/users/jgreener64/gists{/gist_id}","starred_url":"https://api.github.com/users/jgreener64/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jgreener64/subscriptions","organizations_url":"https://api.github.com/users/jgreener64/orgs","repos_url":"https://api.github.com/users/jgreener64/repos","events_url":"https://api.github.com/users/jgreener64/events{/privacy}","received_events_url":"https://api.github.com/users/jgreener64/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-08-07T16:39:14Z","updated_at":"2017-08-07T17:46:38Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biopython/biopython/pulls/1358","html_url":"https://github.com/biopython/biopython/pull/1358","diff_url":"https://github.com/biopython/biopython/pull/1358.diff","patch_url":"https://github.com/biopython/biopython/pull/1358.patch"},"body":"I have seen in some comments on here that the use of `shlex` to split the lines in mmCIF parsing is slow, and I also found an error due to this.\r\n\r\nThis PR replaces `shlex.split` with a custom function to split lines. On my machine it gives 3-4x speedups in the construction of `MMCIF2Dict`.\r\n\r\nLet me know if this is suitable and if any changes are required.\r\n\r\nThis pull request addresses issue #1357.\r\n\r\nI hereby agree to dual licence this and any previous contributions under both\r\nthe _Biopython License Agreement_ AND the _BSD 3-Clause License_.\r\n\r\nI am happy to be thanked by name in the ``NEWS.rst`` and\r\n``CONTRIB.rst`` files.\r\n\r\nI have read the ``CONTRIBUTING.rst`` file and understand that AppVeyor and\r\nTravisCI will be used to confirm the Biopython unit tests and ``flake8`` style\r\nchecks pass with these changes.\r\n"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/320732118","html_url":"https://github.com/biopython/biopython/pull/1358#issuecomment-320732118","issue_url":"https://api.github.com/repos/biopython/biopython/issues/1358","id":320732118,"user":{"login":"codecov[bot]","id":22429695,"avatar_url":"https://avatars2.githubusercontent.com/in/254?v=4","gravatar_id":"","url":"https://api.github.com/users/codecov%5Bbot%5D","html_url":"https://github.com/apps/codecov","followers_url":"https://api.github.com/users/codecov%5Bbot%5D/followers","following_url":"https://api.github.com/users/codecov%5Bbot%5D/following{/other_user}","gists_url":"https://api.github.com/users/codecov%5Bbot%5D/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov%5Bbot%5D/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov%5Bbot%5D/subscriptions","organizations_url":"https://api.github.com/users/codecov%5Bbot%5D/orgs","repos_url":"https://api.github.com/users/codecov%5Bbot%5D/repos","events_url":"https://api.github.com/users/codecov%5Bbot%5D/events{/privacy}","received_events_url":"https://api.github.com/users/codecov%5Bbot%5D/received_events","type":"Bot","site_admin":false},"created_at":"2017-08-07T17:46:38Z","updated_at":"2017-08-07T17:46:38Z","body":"# [Codecov](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=h1) Report\n> Merging [#1358](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=desc) into [master](https://codecov.io/gh/biopython/biopython/commit/6e539988b384e3d848256b3921bb6de93d972590?src=pr&el=desc) will **decrease** coverage by `<.01%`.\n> The diff coverage is `100%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/biopython/biopython/pull/1358/graphs/tree.svg?width=650&height=150&src=pr&token=x1lNrIYszs)](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=tree)\n\n```diff\n@@            Coverage Diff             @@\n##           master    #1358      +/-   ##\n==========================================\n- Coverage   84.49%   84.49%   -0.01%     \n==========================================\n  Files         319      319              \n  Lines       48920    48945      +25     \n==========================================\n+ Hits        41336    41357      +21     \n- Misses       7584     7588       +4\n```\n\n\n| [Impacted Files](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=tree) | Coverage Δ | |\n|---|---|---|\n| [Bio/PDB/MMCIF2Dict.py](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=tree#diff-QmlvL1BEQi9NTUNJRjJEaWN0LnB5) | `100% <100%> (ø)` | :arrow_up: |\n| [Bio/GA/Evolver.py](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=tree#diff-QmlvL0dBL0V2b2x2ZXIucHk=) | `54.54% <0%> (-18.19%)` | :arrow_down: |\n\n------\n\n[Continue to review full report at Codecov](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=continue).\n> **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta)\n> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`\n> Powered by [Codecov](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=footer). Last update [6e53998...a81362c](https://codecov.io/gh/biopython/biopython/pull/1358?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).\n"}}
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