{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/925","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/925/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/925/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/925/events","html_url":"https://github.com/biocore/scikit-bio/pull/925","id":76081060,"number":925,"title":"Update OrdinationResults class","user":{"login":"ElDeveloper","id":375307,"avatar_url":"https://avatars.githubusercontent.com/u/375307?v=3","gravatar_id":"","url":"https://api.github.com/users/ElDeveloper","html_url":"https://github.com/ElDeveloper","followers_url":"https://api.github.com/users/ElDeveloper/followers","following_url":"https://api.github.com/users/ElDeveloper/following{/other_user}","gists_url":"https://api.github.com/users/ElDeveloper/gists{/gist_id}","starred_url":"https://api.github.com/users/ElDeveloper/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ElDeveloper/subscriptions","organizations_url":"https://api.github.com/users/ElDeveloper/orgs","repos_url":"https://api.github.com/users/ElDeveloper/repos","events_url":"https://api.github.com/users/ElDeveloper/events{/privacy}","received_events_url":"https://api.github.com/users/ElDeveloper/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/biocore/scikit-bio/labels/DO%20NOT%20MERGE","name":"DO NOT MERGE","color":"e11d21"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/scikit-bio/milestones/11","html_url":"https://github.com/biocore/scikit-bio/milestones/0.4.0:%20Beta%20Release","labels_url":"https://api.github.com/repos/biocore/scikit-bio/milestones/11/labels","id":802955,"number":11,"title":"0.4.0: Beta Release","description":"Initial beta release to correspond with SciPy 2015. Release includes API that is marked stable, experimental (unstable), and deprecated.","creator":{"login":"ebolyen","id":3976804,"avatar_url":"https://avatars.githubusercontent.com/u/3976804?v=3","gravatar_id":"","url":"https://api.github.com/users/ebolyen","html_url":"https://github.com/ebolyen","followers_url":"https://api.github.com/users/ebolyen/followers","following_url":"https://api.github.com/users/ebolyen/following{/other_user}","gists_url":"https://api.github.com/users/ebolyen/gists{/gist_id}","starred_url":"https://api.github.com/users/ebolyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebolyen/subscriptions","organizations_url":"https://api.github.com/users/ebolyen/orgs","repos_url":"https://api.github.com/users/ebolyen/repos","events_url":"https://api.github.com/users/ebolyen/events{/privacy}","received_events_url":"https://api.github.com/users/ebolyen/received_events","type":"User","site_admin":false},"open_issues":30,"closed_issues":0,"state":"open","created_at":"2014-09-25T17:43:20Z","updated_at":"2015-06-18T23:31:51Z","due_on":"2015-06-30T07:00:00Z","closed_at":null},"comments":17,"created_at":"2015-05-13T18:34:48Z","updated_at":"2015-06-19T00:02:14Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/925","html_url":"https://github.com/biocore/scikit-bio/pull/925","diff_url":"https://github.com/biocore/scikit-bio/pull/925.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/925.patch"},"body":"**Do not merge**\r\n\r\nFixes #521\r\n\r\nto-do before merge:\r\n\r\n- [x] update PCoA method and tests (@jairideout)\r\n- [x] update RDA method and tests (@mortonjt)\r\n- [x] update CA method and tests (@ElDeveloper)\r\n- [x] update CCA method and tests (@josenavas / @mortonjt)\r\n- [x] fix broken `OrdinationResults.__str__` method and update tests to catch this failure\r\n- [ ] fix coverage issues (definitely `skbio.util.assert_ordination_results_equal`, possibly others). Rewrite unit tests to cover new keyword arguments (@ebolyen)\r\n- [ ] test methods against vegan package test data. Important: make sure the constrained methods (CCA, RDA) either 1) report *only* constrained axes **OR** 2) if they report both constrained and unconstrained axes, the axes are labeled correctly.\r\n- [x] get all tests to pass\r\n- [ ] investigate using `scipy.linalg` wherever `numpy.linalg` is used (see [here](http://docs.scipy.org/doc/scipy/reference/tutorial/linalg.html#scipy-linalg-vs-numpy-linalg) for reasons why we want to do this)\r\n- [ ] detailed review from anyone available\r\n- [ ] ask @Jorge-C to review specific sections of the docs (ideally all changes if possible). We'll add comments to specific parts of the docs that need review"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/113322292","html_url":"https://github.com/biocore/scikit-bio/pull/925#issuecomment-113322292","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/925","id":113322292,"user":{"login":"ebolyen","id":3976804,"avatar_url":"https://avatars.githubusercontent.com/u/3976804?v=3","gravatar_id":"","url":"https://api.github.com/users/ebolyen","html_url":"https://github.com/ebolyen","followers_url":"https://api.github.com/users/ebolyen/followers","following_url":"https://api.github.com/users/ebolyen/following{/other_user}","gists_url":"https://api.github.com/users/ebolyen/gists{/gist_id}","starred_url":"https://api.github.com/users/ebolyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ebolyen/subscriptions","organizations_url":"https://api.github.com/users/ebolyen/orgs","repos_url":"https://api.github.com/users/ebolyen/repos","events_url":"https://api.github.com/users/ebolyen/events{/privacy}","received_events_url":"https://api.github.com/users/ebolyen/received_events","type":"User","site_admin":false},"created_at":"2015-06-19T00:02:14Z","updated_at":"2015-06-19T00:02:14Z","body":"Did you `make clean` that's usually the cause when I see that error.\nAlthough that path hasn't actually changed so it doesn't make a lot of\nsense.\n\nOn Thu, Jun 18, 2015 at 5:00 PM, mortonjt <notifications@github.com> wrote:\n\n> I just made the following changes\n>\n>    - Cleaned up the test cases for CA, CCA and RDA\n>    - Removed the vegan test cases. They are redundant and don't add\n>    anything new to the testing suite. Also, I'm not even sure if they would be\n>    BSD compatible\n>    - Swapped out np.linalg with scipy.linalg. They give identical\n>    results. scipy.linalg will typically be faster for new users.\n>\n> I'm still getting a weird error with sphinx - not sure what is going on\n> there.\n>\n> /Users/mortonjt/Documents/software/python/scikit-bio/doc/source/generated/generated/skbio.stats.distance.DissimilarityMatrix.rst:59: WARNING: toctree references unknown document u'generated/generated/skbio.stats.distance.DissimilarityMatrix.data'\n>\n> Finally, @Jorge-C <https://github.com/Jorge-C> is investigating the bug\n> with the miscalculated eigenvalues. He'll be submitting to this PR in a bit.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/biocore/scikit-bio/pull/925#issuecomment-113322123>.\n>\n"}}