{"action":"created","issue":{"url":"https://api.github.com/repos/edickie/ciftify/issues/66","repository_url":"https://api.github.com/repos/edickie/ciftify","labels_url":"https://api.github.com/repos/edickie/ciftify/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/edickie/ciftify/issues/66/comments","events_url":"https://api.github.com/repos/edickie/ciftify/issues/66/events","html_url":"https://github.com/edickie/ciftify/issues/66","id":333503941,"node_id":"MDU6SXNzdWUzMzM1MDM5NDE=","number":66,"title":"bug in 2.0.3","user":{"login":"oricon","id":8575279,"node_id":"MDQ6VXNlcjg1NzUyNzk=","avatar_url":"https://avatars3.githubusercontent.com/u/8575279?v=4","gravatar_id":"","url":"https://api.github.com/users/oricon","html_url":"https://github.com/oricon","followers_url":"https://api.github.com/users/oricon/followers","following_url":"https://api.github.com/users/oricon/following{/other_user}","gists_url":"https://api.github.com/users/oricon/gists{/gist_id}","starred_url":"https://api.github.com/users/oricon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oricon/subscriptions","organizations_url":"https://api.github.com/users/oricon/orgs","repos_url":"https://api.github.com/users/oricon/repos","events_url":"https://api.github.com/users/oricon/events{/privacy}","received_events_url":"https://api.github.com/users/oricon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"DESm1th","id":10541496,"node_id":"MDQ6VXNlcjEwNTQxNDk2","avatar_url":"https://avatars2.githubusercontent.com/u/10541496?v=4","gravatar_id":"","url":"https://api.github.com/users/DESm1th","html_url":"https://github.com/DESm1th","followers_url":"https://api.github.com/users/DESm1th/followers","following_url":"https://api.github.com/users/DESm1th/following{/other_user}","gists_url":"https://api.github.com/users/DESm1th/gists{/gist_id}","starred_url":"https://api.github.com/users/DESm1th/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DESm1th/subscriptions","organizations_url":"https://api.github.com/users/DESm1th/orgs","repos_url":"https://api.github.com/users/DESm1th/repos","events_url":"https://api.github.com/users/DESm1th/events{/privacy}","received_events_url":"https://api.github.com/users/DESm1th/received_events","type":"User","site_admin":false},"assignees":[{"login":"DESm1th","id":10541496,"node_id":"MDQ6VXNlcjEwNTQxNDk2","avatar_url":"https://avatars2.githubusercontent.com/u/10541496?v=4","gravatar_id":"","url":"https://api.github.com/users/DESm1th","html_url":"https://github.com/DESm1th","followers_url":"https://api.github.com/users/DESm1th/followers","following_url":"https://api.github.com/users/DESm1th/following{/other_user}","gists_url":"https://api.github.com/users/DESm1th/gists{/gist_id}","starred_url":"https://api.github.com/users/DESm1th/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DESm1th/subscriptions","organizations_url":"https://api.github.com/users/DESm1th/orgs","repos_url":"https://api.github.com/users/DESm1th/repos","events_url":"https://api.github.com/users/DESm1th/events{/privacy}","received_events_url":"https://api.github.com/users/DESm1th/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2018-06-19T03:09:13Z","updated_at":"2018-06-23T22:30:27Z","closed_at":null,"author_association":"NONE","body":"I think there might be a bug in the latest update. I tried installed the update with pip but there was an error. (I replicated the problem on another computer with Python 3.6.5)\r\n\r\n> Successfully built ciftify\r\n> Installing collected packages: ciftify\r\n> Exception:\r\n> Traceback (most recent call last):\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/basecommand.py\", line 228, in main\r\n>     status = self.run(options, args)\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/commands/install.py\", line 335, in run\r\n>     use_user_site=options.use_user_site,\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/__init__.py\", line 49, in install_given_reqs\r\n>     **kwargs\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/req_install.py\", line 748, in install\r\n>     use_user_site=use_user_site, pycompile=pycompile,\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/req_install.py\", line 961, in move_wheel_files\r\n>     warn_script_location=warn_script_location,\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/wheel.py\", line 327, in move_wheel_files\r\n>     console, gui = get_entrypoints(ep_file)\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/wheel.py\", line 143, in get_entrypoints\r\n>     console = dict(_split_ep(v) for v in console.values())\r\n> ValueError: dictionary update sequence element #4 has length 3; 2 is required\r\n\r\nSo I did a manual install and still have an issue running commands:\r\n\r\n> [joseph.orr@gfx bin$ ciftify_subject_fmri --SmoothingFWHM 2 --ciftify-work-dir $outdir --already-in-MNI $func $subject $label\r\n> Fatal Python error: Py_Initialize: can't initialize sys standard streams\r\n> Traceback (most recent call last):\r\n>   File \"/apps/psyc/ciftify/2.0.3/ciftify/io.py\", line 9, in <module>\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/logging/__init__.py\", line 26, in <module>\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/traceback.py\", line 5, in <module>\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/linecache.py\", line 11, in <module>\r\n>   File \"/apps/psyc/anaconda3/python35_520/lib/python3.6/tokenize.py\", line 27, in <module>\r\n> ImportError: cannot import name 'open'\r\n> Aborted (core dumped)"},"comment":{"url":"https://api.github.com/repos/edickie/ciftify/issues/comments/399714726","html_url":"https://github.com/edickie/ciftify/issues/66#issuecomment-399714726","issue_url":"https://api.github.com/repos/edickie/ciftify/issues/66","id":399714726,"node_id":"MDEyOklzc3VlQ29tbWVudDM5OTcxNDcyNg==","user":{"login":"edickie","id":13203958,"node_id":"MDQ6VXNlcjEzMjAzOTU4","avatar_url":"https://avatars1.githubusercontent.com/u/13203958?v=4","gravatar_id":"","url":"https://api.github.com/users/edickie","html_url":"https://github.com/edickie","followers_url":"https://api.github.com/users/edickie/followers","following_url":"https://api.github.com/users/edickie/following{/other_user}","gists_url":"https://api.github.com/users/edickie/gists{/gist_id}","starred_url":"https://api.github.com/users/edickie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edickie/subscriptions","organizations_url":"https://api.github.com/users/edickie/orgs","repos_url":"https://api.github.com/users/edickie/repos","events_url":"https://api.github.com/users/edickie/events{/privacy}","received_events_url":"https://api.github.com/users/edickie/received_events","type":"User","site_admin":false},"created_at":"2018-06-23T22:30:26Z","updated_at":"2018-06-23T22:30:26Z","author_association":"OWNER","body":"oops sorry. It looks like the final bug fixes were not included in the\n2.0.4 release. 2.0.5 has been pushed.\n\n\n\nOn Sat, Jun 23, 2018 at 5:09 PM, Joseph M. Orr <notifications@github.com>\nwrote:\n\n> Hi the install works without a problem, but now I run into an error with\n> niio in ciftify_subject_fmri when it gets to the Subcortical Processing:\n>\n> Traceback (most recent call last):\n> File \"/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri\", line\n> 1062, in\n> main()\n> File \"/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri\", line\n> 1057, in main\n> ret = run_ciftify_subject_fmri(settings, tmpdir)\n> File \"/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri\", line\n> 190, in run_ciftify_subject_fmri\n> tmpdir)\n> File \"/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri\", line\n> 893, in subcortical_atlas\n> func_vx_size = ciftify.niio.voxel_spacing(input_fMRI)\n> AttributeError: module 'ciftify' has no attribute 'niio'\n> Here's the last line of the ciftify_subject_fmri.log: 2018-06-23\n> 15:53:57.789319 : Subcortical Processing\n>\n> VolumefMRI: /fdata/scratch/joseph.orr/adaptcog/fmri/hcp/sub-\n> M80301092/MNINonLinear/Results/task-ritl_acq-MB_run-\n> 01/task-ritl_acq-MB_run-01.nii.gz\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/edickie/ciftify/issues/66#issuecomment-399710810>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/AMl59pDIeWdfRRyoQyRFdism52dPSJGZks5t_q5_gaJpZM4Usx09>\n> .\n>\n"}}
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