{"action":"created","issue":{"url":"https://api.github.com/repos/YosefLab/scVI/issues/204","repository_url":"https://api.github.com/repos/YosefLab/scVI","labels_url":"https://api.github.com/repos/YosefLab/scVI/issues/204/labels{/name}","comments_url":"https://api.github.com/repos/YosefLab/scVI/issues/204/comments","events_url":"https://api.github.com/repos/YosefLab/scVI/issues/204/events","html_url":"https://github.com/YosefLab/scVI/issues/204","id":371324404,"node_id":"MDU6SXNzdWUzNzEzMjQ0MDQ=","number":204,"title":"tox errors","user":{"login":"jeff-regier","id":8953355,"node_id":"MDQ6VXNlcjg5NTMzNTU=","avatar_url":"https://avatars2.githubusercontent.com/u/8953355?v=4","gravatar_id":"","url":"https://api.github.com/users/jeff-regier","html_url":"https://github.com/jeff-regier","followers_url":"https://api.github.com/users/jeff-regier/followers","following_url":"https://api.github.com/users/jeff-regier/following{/other_user}","gists_url":"https://api.github.com/users/jeff-regier/gists{/gist_id}","starred_url":"https://api.github.com/users/jeff-regier/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeff-regier/subscriptions","organizations_url":"https://api.github.com/users/jeff-regier/orgs","repos_url":"https://api.github.com/users/jeff-regier/repos","events_url":"https://api.github.com/users/jeff-regier/events{/privacy}","received_events_url":"https://api.github.com/users/jeff-regier/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jules-samaran","id":42657542,"node_id":"MDQ6VXNlcjQyNjU3NTQy","avatar_url":"https://avatars2.githubusercontent.com/u/42657542?v=4","gravatar_id":"","url":"https://api.github.com/users/jules-samaran","html_url":"https://github.com/jules-samaran","followers_url":"https://api.github.com/users/jules-samaran/followers","following_url":"https://api.github.com/users/jules-samaran/following{/other_user}","gists_url":"https://api.github.com/users/jules-samaran/gists{/gist_id}","starred_url":"https://api.github.com/users/jules-samaran/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jules-samaran/subscriptions","organizations_url":"https://api.github.com/users/jules-samaran/orgs","repos_url":"https://api.github.com/users/jules-samaran/repos","events_url":"https://api.github.com/users/jules-samaran/events{/privacy}","received_events_url":"https://api.github.com/users/jules-samaran/received_events","type":"User","site_admin":false},"assignees":[{"login":"jules-samaran","id":42657542,"node_id":"MDQ6VXNlcjQyNjU3NTQy","avatar_url":"https://avatars2.githubusercontent.com/u/42657542?v=4","gravatar_id":"","url":"https://api.github.com/users/jules-samaran","html_url":"https://github.com/jules-samaran","followers_url":"https://api.github.com/users/jules-samaran/followers","following_url":"https://api.github.com/users/jules-samaran/following{/other_user}","gists_url":"https://api.github.com/users/jules-samaran/gists{/gist_id}","starred_url":"https://api.github.com/users/jules-samaran/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jules-samaran/subscriptions","organizations_url":"https://api.github.com/users/jules-samaran/orgs","repos_url":"https://api.github.com/users/jules-samaran/repos","events_url":"https://api.github.com/users/jules-samaran/events{/privacy}","received_events_url":"https://api.github.com/users/jules-samaran/received_events","type":"User","site_admin":false}],"milestone":null,"comments":8,"created_at":"2018-10-18T01:17:01Z","updated_at":"2018-10-29T17:19:36Z","closed_at":null,"author_association":"COLLABORATOR","body":"The unit tests run by `tox` are failing. I don't think we can update the version of scvi available through pip (issue #202) until they pass.\r\n\r\nIt looks like the error is coming from `test_notebooks`, due to a path issue for the line `import docs.notebooks.annotation`.\r\n\r\nThis is the basic idea behind tox: https://tox.readthedocs.io/en/latest/\r\nAnd I pasted a sample run of tox below, after adding `jupyter >= 1.0` to setup.py.\r\n\r\n@jules-samaran: Can you figure out how to fix this issue?\r\n\r\n\r\n```\r\nJeffreys-MBP-3:scVI jeff$ tox\r\nGLOB sdist-make: /Users/jeff/git/scVI/setup.py\r\npy37 inst-nodeps: /Users/jeff/git/scVI/.tox/.tmp/package/1/scvi-0.2.2.zip\r\n...\r\n___________________________________________________ test_notebooks ___________________________________________________\r\n\r\n    def test_notebooks():\r\n        prefix = 'annotation'\r\n        # if exists, save and overwrite\r\n        config_filename = prefix + '.config.json'  # By default, benchmark config, but overridden for tests\r\n        config_filename_tmp = prefix + '.config.tmp.json'\r\n    \r\n        # Save content in memory in tmp file\r\n        existing_config_to_restore = os.path.exists(path + config_filename)\r\n        if existing_config_to_restore:\r\n            shutil.copy(path + config_filename, path + config_filename_tmp)\r\n    \r\n        # Overwritting\r\n        shutil.copy(test_path + config_filename, path + config_filename)\r\n        try:\r\n>           import docs.notebooks.annotation\r\nE           ModuleNotFoundError: No module named 'docs'\r\n\r\ntests/test_notebook.py:119: ModuleNotFoundError\r\n```"},"comment":{"url":"https://api.github.com/repos/YosefLab/scVI/issues/comments/433999074","html_url":"https://github.com/YosefLab/scVI/issues/204#issuecomment-433999074","issue_url":"https://api.github.com/repos/YosefLab/scVI/issues/204","id":433999074,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMzk5OTA3NA==","user":{"login":"jules-samaran","id":42657542,"node_id":"MDQ6VXNlcjQyNjU3NTQy","avatar_url":"https://avatars2.githubusercontent.com/u/42657542?v=4","gravatar_id":"","url":"https://api.github.com/users/jules-samaran","html_url":"https://github.com/jules-samaran","followers_url":"https://api.github.com/users/jules-samaran/followers","following_url":"https://api.github.com/users/jules-samaran/following{/other_user}","gists_url":"https://api.github.com/users/jules-samaran/gists{/gist_id}","starred_url":"https://api.github.com/users/jules-samaran/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jules-samaran/subscriptions","organizations_url":"https://api.github.com/users/jules-samaran/orgs","repos_url":"https://api.github.com/users/jules-samaran/repos","events_url":"https://api.github.com/users/jules-samaran/events{/privacy}","received_events_url":"https://api.github.com/users/jules-samaran/received_events","type":"User","site_admin":false},"created_at":"2018-10-29T17:19:35Z","updated_at":"2018-10-29T17:19:35Z","author_association":"COLLABORATOR","body":"We do not have to add jupyter to setup.py we can just add it in tox.ini to the list of things tox installs in the environment it creates to run the tests.\r\nLast week I tried moving the notebooks to the tests directory but I remember it didn't work, I'm going to try again to make sure but I had another idea, considering that running make tests successfully tests the notebook by 'importing them as modules' and running their code, we might ask tox to run the make tests command instead of pytest"}}
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