{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/American-Gut/issues/185","labels_url":"https://api.github.com/repos/biocore/American-Gut/issues/185/labels{/name}","comments_url":"https://api.github.com/repos/biocore/American-Gut/issues/185/comments","events_url":"https://api.github.com/repos/biocore/American-Gut/issues/185/events","html_url":"https://github.com/biocore/American-Gut/pull/185","id":124312021,"number":185,"title":"WIP: Per sample alpha plots","user":{"login":"JWDebelius","id":5534846,"avatar_url":"https://avatars.githubusercontent.com/u/5534846?v=3","gravatar_id":"","url":"https://api.github.com/users/JWDebelius","html_url":"https://github.com/JWDebelius","followers_url":"https://api.github.com/users/JWDebelius/followers","following_url":"https://api.github.com/users/JWDebelius/following{/other_user}","gists_url":"https://api.github.com/users/JWDebelius/gists{/gist_id}","starred_url":"https://api.github.com/users/JWDebelius/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JWDebelius/subscriptions","organizations_url":"https://api.github.com/users/JWDebelius/orgs","repos_url":"https://api.github.com/users/JWDebelius/repos","events_url":"https://api.github.com/users/JWDebelius/events{/privacy}","received_events_url":"https://api.github.com/users/JWDebelius/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-12-30T06:58:03Z","updated_at":"2015-12-30T07:00:28Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biocore/American-Gut/pulls/185","html_url":"https://github.com/biocore/American-Gut/pull/185","diff_url":"https://github.com/biocore/American-Gut/pull/185.diff","patch_url":"https://github.com/biocore/American-Gut/pull/185.patch"},"body":"Depends on #182.\r\n\r\nGiven that the long term plan is to introduce a regression model and shading (if possible). This will require a helper function. It will be absolutely necessary to have tests in place for this function.\r\n\r\nThe current code is lightweight plotting code. I'm debating passing a debug flag to check that the early logic statements are returning correctly, but most are either core libraries or pandas IO.\r\n\r\nI'm not sure if this is better to write as a click command, or as a straight python command that can be imported. I imagine a click command will have to be wrapped in `per_sample.py`, with something similar to the [`gradient_pcoa`](https://github.com/biocore/American-Gut/blob/master/americangut/per_sample.py#L368) function. My concern has to do with writing an appropriate test for the click command, although this can be pushed back. I'm not familiar with this framework, but that's not a good reason not to use it.\r\n\r\nThe alternative is to run it as a straight python command, and modifying the [`09-per-participants-results`](https://github.com/biocore/American-Gut/blob/master/ipynb/primary-processing/09-per_participant_results.md) notebook."},"comment":{"url":"https://api.github.com/repos/biocore/American-Gut/issues/comments/167947215","html_url":"https://github.com/biocore/American-Gut/pull/185#issuecomment-167947215","issue_url":"https://api.github.com/repos/biocore/American-Gut/issues/185","id":167947215,"user":{"login":"wasade","id":474290,"avatar_url":"https://avatars.githubusercontent.com/u/474290?v=3","gravatar_id":"","url":"https://api.github.com/users/wasade","html_url":"https://github.com/wasade","followers_url":"https://api.github.com/users/wasade/followers","following_url":"https://api.github.com/users/wasade/following{/other_user}","gists_url":"https://api.github.com/users/wasade/gists{/gist_id}","starred_url":"https://api.github.com/users/wasade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wasade/subscriptions","organizations_url":"https://api.github.com/users/wasade/orgs","repos_url":"https://api.github.com/users/wasade/repos","events_url":"https://api.github.com/users/wasade/events{/privacy}","received_events_url":"https://api.github.com/users/wasade/received_events","type":"User","site_admin":false},"created_at":"2015-12-30T07:00:28Z","updated_at":"2015-12-30T07:00:28Z","body":"Executing as a function in 09 would save a lot of overhead\nOn Dec 29, 2015 10:58 PM, \"J W Debelius\" <notifications@github.com> wrote:\n\n> Depends on #182 <https://github.com/biocore/American-Gut/pull/182>.\n>\n> Given that the long term plan is to introduce a regression model and\n> shading (if possible). This will require a helper function. It will be\n> absolutely necessary to have tests in place for this function.\n>\n> The current code is lightweight plotting code. I'm debating passing a\n> debug flag to check that the early logic statements are returning\n> correctly, but most are either core libraries or pandas IO.\n>\n> I'm not sure if this is better to write as a click command, or as a\n> straight python command that can be imported. I imagine a click command\n> will have to be wrapped in per_sample.py, with something similar to the\n> gradient_pcoa\n> <https://github.com/biocore/American-Gut/blob/master/americangut/per_sample.py#L368>\n> function. My concern has to do with writing an appropriate test for the\n> click command, although this can be pushed back. I'm not familiar with this\n> framework, but that's not a good reason not to use it.\n>\n> The alternative is to run it as a straight python command, and modifying\n> the 09-per-participants-results\n> <https://github.com/biocore/American-Gut/blob/master/ipynb/primary-processing/09-per_participant_results.md>\n> notebook.\n> ------------------------------\n> You can view, comment on, or merge this pull request online at:\n>\n>   https://github.com/biocore/American-Gut/pull/185\n> Commit Summary\n>\n>    - Code to create alpha diversity plots\n>    - Updates collapse to include alpha diversity\n>    - Adds click command to ag_alpha_plots\n>    - Removes the test file for a non-click command\n>\n> File Changes\n>\n>    - *A* americangut/ag_alpha_plots.py\n>    <https://github.com/biocore/American-Gut/pull/185/files#diff-0> (186)\n>    - *M* americangut/notebook_environment.py\n>    <https://github.com/biocore/American-Gut/pull/185/files#diff-1> (8)\n>    - *M* ipynb/primary-processing/08-collapse_samples.md\n>    <https://github.com/biocore/American-Gut/pull/185/files#diff-2> (37)\n>\n> Patch Links:\n>\n>    - https://github.com/biocore/American-Gut/pull/185.patch\n>    - https://github.com/biocore/American-Gut/pull/185.diff\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/biocore/American-Gut/pull/185>.\n>\n"}}