{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/1384","repository_url":"https://api.github.com/repos/dib-lab/khmer","labels_url":"https://api.github.com/repos/dib-lab/khmer/issues/1384/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/khmer/issues/1384/comments","events_url":"https://api.github.com/repos/dib-lab/khmer/issues/1384/events","html_url":"https://github.com/dib-lab/khmer/issues/1384","id":160104214,"number":1384,"title":"screed test failure","user":{"login":"wwood","id":15348,"avatar_url":"https://avatars.githubusercontent.com/u/15348?v=3","gravatar_id":"","url":"https://api.github.com/users/wwood","html_url":"https://github.com/wwood","followers_url":"https://api.github.com/users/wwood/followers","following_url":"https://api.github.com/users/wwood/following{/other_user}","gists_url":"https://api.github.com/users/wwood/gists{/gist_id}","starred_url":"https://api.github.com/users/wwood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wwood/subscriptions","organizations_url":"https://api.github.com/users/wwood/orgs","repos_url":"https://api.github.com/users/wwood/repos","events_url":"https://api.github.com/users/wwood/events{/privacy}","received_events_url":"https://api.github.com/users/wwood/received_events","type":"User","site_admin":false},"labels":[{"id":149168478,"url":"https://api.github.com/repos/dib-lab/khmer/labels/screed","name":"screed","color":"006b75","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/dib-lab/khmer/milestones/15","html_url":"https://github.com/dib-lab/khmer/milestone/15","labels_url":"https://api.github.com/repos/dib-lab/khmer/milestones/15/labels","id":1179362,"number":15,"title":"screed 1.0","description":"","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":10,"closed_issues":6,"state":"open","created_at":"2015-06-24T14:30:55Z","updated_at":"2016-12-19T22:41:08Z","due_on":null,"closed_at":null},"comments":3,"created_at":"2016-06-14T06:07:49Z","updated_at":"2016-12-19T22:47:54Z","closed_at":null,"body":"Hi,\n\nI'm attempting to package screed and khmer for GNU Guix. I came across this error when running the screed tests. On first glance, it seems the test is streaming in gzip data when the reader explicitly disallows it. So is this an expected failure? All the other tests pass.\n\nThis is with the 0.9 code from pypi.\n\n```\n======================================================================\nERROR: screed.tests.test_streaming.test_stream_fa_gz\n----------------------------------------------------------------------\nTraceback (most recent call last):\n  File \"/gnu/store/4addsbkghgygd9l857zk4issfjmjq9ya-python-nose-1.3.7/lib/python3.4/site-packages/nose-1.3.7-py3.4.egg/nose/case.py\", line 198, in runTest\n    self.test(*self.arg)\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 72, in test_stream_fa_gz\n    streamer(utils.get_test_data('test.fa.gz'))\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 59, in streamer\n    raise exception[0]\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 24, in streamer_reader\n    for read in screed.open(ifilename):\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/openscreed.py\", line 48, in __init__\n    self.iter_fn = self.open_reader(filename, *args, **kwargs)\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/openscreed.py\", line 80, in open_reader\n    first\")\nValueError: gziped data not streamable, pipe through zcat                                 first\n\n======================================================================\nERROR: screed.tests.test_streaming.test_stream_fq_gz\n----------------------------------------------------------------------\nTraceback (most recent call last):\n  File \"/gnu/store/4addsbkghgygd9l857zk4issfjmjq9ya-python-nose-1.3.7/lib/python3.4/site-packages/nose-1.3.7-py3.4.egg/nose/case.py\", line 198, in runTest\n    self.test(*self.arg)\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 85, in test_stream_fq_gz\n    streamer(utils.get_test_data('test.fastq.gz'))\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 59, in streamer\n    raise exception[0]\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/tests/test_streaming.py\", line 24, in streamer_reader\n    for read in screed.open(ifilename):\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/openscreed.py\", line 48, in __init__\n    self.iter_fn = self.open_reader(filename, *args, **kwargs)\n  File \"/tmp/nix-build-python-screed-0.9.drv-5/screed-0.9/screed/openscreed.py\", line 80, in open_reader\n    first\")\nValueError: gziped data not streamable, pipe through zcat                                 first\n\n----------------------------------------------------------------------\n```\n\nThanks,\nben\n"},"comment":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/comments/268101361","html_url":"https://github.com/dib-lab/khmer/issues/1384#issuecomment-268101361","issue_url":"https://api.github.com/repos/dib-lab/khmer/issues/1384","id":268101361,"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":"2016-12-19T22:47:54Z","updated_at":"2016-12-19T22:47:54Z","body":"@luizirber this seems to have been fixed along the way - at least, `python setup.py test` now works. Can you confirm & shall I close as fixed?"}}
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