{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/1214","labels_url":"https://api.github.com/repos/dib-lab/khmer/issues/1214/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/khmer/issues/1214/comments","events_url":"https://api.github.com/repos/dib-lab/khmer/issues/1214/events","html_url":"https://github.com/dib-lab/khmer/pull/1214","id":98273517,"number":1214,"title":"Cleaning up automatic argument setting","user":{"login":"bocajnotnef","id":2142082,"avatar_url":"https://avatars.githubusercontent.com/u/2142082?v=3","gravatar_id":"","url":"https://api.github.com/users/bocajnotnef","html_url":"https://github.com/bocajnotnef","followers_url":"https://api.github.com/users/bocajnotnef/followers","following_url":"https://api.github.com/users/bocajnotnef/following{/other_user}","gists_url":"https://api.github.com/users/bocajnotnef/gists{/gist_id}","starred_url":"https://api.github.com/users/bocajnotnef/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bocajnotnef/subscriptions","organizations_url":"https://api.github.com/users/bocajnotnef/orgs","repos_url":"https://api.github.com/users/bocajnotnef/repos","events_url":"https://api.github.com/users/bocajnotnef/events{/privacy}","received_events_url":"https://api.github.com/users/bocajnotnef/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/dib-lab/khmer/milestones/11","html_url":"https://github.com/dib-lab/khmer/milestones/2.0","labels_url":"https://api.github.com/repos/dib-lab/khmer/milestones/11/labels","id":695846,"number":11,"title":"2.0","description":"Issues that will break the API/file format and so must wait until 2.0.\r\n","creator":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"open_issues":32,"closed_issues":49,"state":"open","created_at":"2014-06-19T14:06:19Z","updated_at":"2015-08-05T17:09:25Z","due_on":null,"closed_at":null},"comments":46,"created_at":"2015-07-30T21:53:23Z","updated_at":"2015-08-06T13:25:49Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/dib-lab/khmer/pulls/1214","html_url":"https://github.com/dib-lab/khmer/pull/1214","diff_url":"https://github.com/dib-lab/khmer/pull/1214.diff","patch_url":"https://github.com/dib-lab/khmer/pull/1214.patch"},"body":"Ref #1117 for expansion of automatic memory usage determination, this time based on estimated number of unique k-mers. Inspired by user experience upgrade goals (#732) and hopefully will fix #1179 (dealing with `-U/--unique-kmers`).\r\n\r\nThis resolves @ctb's comment https://github.com/dib-lab/khmer/issues/1117#issuecomment-126351063:\r\n\r\n>OK, well, let's start a new pull request :). Here are a few requested changes:\r\n\r\n> - change do_sanity_checking name to check_fp_rate\r\n> - should this function only be called if -U is set? For now, I think so...\r\n> - change oxutils shortname to oxfuncs, since it's `oxli.functions' you're importing.\r\n> - get rid of \"optimization\" language in comments - it's automatic argument picking, not optimization :)\r\n> (The goal of all of this is to enable script readability.)\r\n\r\n> Is there a reason that this code isn't called generically in create_countgraph/other khmer_args functions? That seems like a better place for it than adding it into each script individually, but I'm probably missing something.\r\n\r\nMy response to the last: \r\n\r\n> The desired_fp rate varies from script to script, which is why we currently call it on a script-by-script basis--that said, it shouldn't be too hard to pass that along to create_countgraph.\r\n\r\nNext steps TBD"},"comment":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/comments/128363038","html_url":"https://github.com/dib-lab/khmer/pull/1214#issuecomment-128363038","issue_url":"https://api.github.com/repos/dib-lab/khmer/issues/1214","id":128363038,"user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2015-08-06T13:25:48Z","updated_at":"2015-08-06T13:25:48Z","body":"This looks pretty nice and clean to me, but I may not have a chance to dig into it today.  My main comment is that I think the script-level testing should be expanded a bit - think about it and let me know what you decide :)."}}