{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/events","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/551","id":119748746,"number":551,"title":"2 failures and 1 error while performing the tests","user":{"login":"ashkurti","id":6951871,"avatar_url":"https://avatars.githubusercontent.com/u/6951871?v=3","gravatar_id":"","url":"https://api.github.com/users/ashkurti","html_url":"https://github.com/ashkurti","followers_url":"https://api.github.com/users/ashkurti/followers","following_url":"https://api.github.com/users/ashkurti/following{/other_user}","gists_url":"https://api.github.com/users/ashkurti/gists{/gist_id}","starred_url":"https://api.github.com/users/ashkurti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashkurti/subscriptions","organizations_url":"https://api.github.com/users/ashkurti/orgs","repos_url":"https://api.github.com/users/ashkurti/repos","events_url":"https://api.github.com/users/ashkurti/events{/privacy}","received_events_url":"https://api.github.com/users/ashkurti/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":55,"created_at":"2015-12-01T16:03:02Z","updated_at":"2015-12-08T17:23:33Z","closed_at":"2015-12-03T17:26:35Z","body":"Hi MDAnalysis developers!!\r\n\r\nAny advice on the following error and failures will be much appreciated. I am aiming to get everything working before contributing to the MDAnalysis code with some analysis enhancements.\r\n```\r\n======================================================================\r\nERROR: MDAnalysisTests.coordinates.test_trz.TestTRZWriter2.test_writer_trz_from_other\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/nose/case.py\", line 197, in runTest\r\n    self.test(*self.arg)\r\n  File \"MDAnalysisTests/coordinates/test_trz.py\", line 189, in test_writer_trz_from_other\r\n    u2 = mda.Universe(two_water_gro, outfile)\r\n  File \"/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py\", line 3791, in __init__\r\n    \"Error: {2}\".format(self.filename, parser, err))\r\nIOError: Failed to load from the topology file MDAnalysisTests/data/two_water_gro.gro with parser <class 'MDAnalysis.topology.GROParser.GROParser'>.\r\nError: [Errno 5] Cannot open file or stream in mode='r'.: \"'MDAnalysisTests/data/two_water_gro.gro'\"\r\n-------------------- >> begin captured stderr << ---------------------\r\n/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRZ.py:539: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory\r\n  \"\".format(\", \".join(faked_attrs)))\r\n/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRZ.py:547: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. \r\n  warnings.warn(\"Timestep didn't have velocity information, \"\r\n\r\n--------------------- >> end captured stderr << ----------------------\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/two_water_gro.gro...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/Amber/bala.ncdf...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmp2QChD0/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/Amber/tz2.truncoct.nc...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmpdfdaTZ/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n----------------------------------------------------------------------\r\nRan 3275 tests in 983.183s\r\n\r\nFAILED (KNOWNFAIL=3, errors=1, failures=2)\r\n```"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/162952079","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/551#issuecomment-162952079","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551","id":162952079,"user":{"login":"ashkurti","id":6951871,"avatar_url":"https://avatars.githubusercontent.com/u/6951871?v=3","gravatar_id":"","url":"https://api.github.com/users/ashkurti","html_url":"https://github.com/ashkurti","followers_url":"https://api.github.com/users/ashkurti/followers","following_url":"https://api.github.com/users/ashkurti/following{/other_user}","gists_url":"https://api.github.com/users/ashkurti/gists{/gist_id}","starred_url":"https://api.github.com/users/ashkurti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashkurti/subscriptions","organizations_url":"https://api.github.com/users/ashkurti/orgs","repos_url":"https://api.github.com/users/ashkurti/repos","events_url":"https://api.github.com/users/ashkurti/events{/privacy}","received_events_url":"https://api.github.com/users/ashkurti/received_events","type":"User","site_admin":false},"created_at":"2015-12-08T17:23:33Z","updated_at":"2015-12-08T17:23:33Z","body":"Ok, I have done every bit, a part from the ```create a PR from that branch in your repo to our develop branch here``` bit. Should I use for this the hub wrapper, or should I upload my forked repository to my github account and then send the PR vi web from there?"}}