{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/1850","labels_url":"https://api.github.com/repos/biocore/qiime/issues/1850/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/1850/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/1850/events","html_url":"https://github.com/biocore/qiime/issues/1850","id":53998745,"number":1850,"title":"numpy deprecation warnings","user":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/biocore/qiime/labels/bug","name":"bug","color":"e10c02"}],"state":"open","locked":false,"assignee":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/biocore/qiime/milestones/21","labels_url":"https://api.github.com/repos/biocore/qiime/milestones/21/labels","id":530599,"number":21,"title":"QIIME 1.9.0","description":"This will likely be the last minor release under QIIME 1. ","creator":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"open_issues":17,"closed_issues":267,"state":"open","created_at":"2014-01-08T19:45:01Z","updated_at":"2015-01-13T20:28:22Z","due_on":"2015-01-21T07:00:00Z","closed_at":null},"comments":14,"created_at":"2015-01-11T17:51:26Z","updated_at":"2015-01-13T21:00:41Z","closed_at":null,"body":"@wasade noted in #1847 that there are numpy deprecation warnings being raised with numpy 1.9.1:\r\n\r\n```\r\n/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2499: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.\r\n  VisibleDeprecationWarning)\r\nError in validate_mapping_file.py: option -m: file does not exist: 'map.tsv'\r\n\r\nIf you need help with QIIME, see:\r\nhttp://help.qiime.org\r\n```\r\n\r\nI think these warnings are coming from PyCogent beta diversity code. It's strange that the warnings are being raised in scripts that aren't related to beta diversty (e.g., validate_mapping_file.py). We should figure out how to suppress these warnings, or at least suppress them for scripts that aren't related to beta diversity.\r\n\r\nNote: I'm not able to reproduce this locally with numpy 1.9.1."},"comment":{"url":"https://api.github.com/repos/biocore/qiime/issues/comments/69818947","html_url":"https://github.com/biocore/qiime/issues/1850#issuecomment-69818947","issue_url":"https://api.github.com/repos/biocore/qiime/issues/1850","id":69818947,"user":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"created_at":"2015-01-13T21:00:41Z","updated_at":"2015-01-13T21:00:41Z","body":"Looking into this further, scipy >= 0.14.0 should work (just verified locally). Updated my pull request to relax the version requirement."}}