{"action":"created","issue":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/39","labels_url":"https://api.github.com/repos/ewels/MultiQC/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/ewels/MultiQC/issues/39/comments","events_url":"https://api.github.com/repos/ewels/MultiQC/issues/39/events","html_url":"https://github.com/ewels/MultiQC/pull/39","id":108278779,"number":39,"title":"Updated cli and logging","user":{"login":"moonso","id":405278,"avatar_url":"https://avatars.githubusercontent.com/u/405278?v=3","gravatar_id":"","url":"https://api.github.com/users/moonso","html_url":"https://github.com/moonso","followers_url":"https://api.github.com/users/moonso/followers","following_url":"https://api.github.com/users/moonso/following{/other_user}","gists_url":"https://api.github.com/users/moonso/gists{/gist_id}","starred_url":"https://api.github.com/users/moonso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/moonso/subscriptions","organizations_url":"https://api.github.com/users/moonso/orgs","repos_url":"https://api.github.com/users/moonso/repos","events_url":"https://api.github.com/users/moonso/events{/privacy}","received_events_url":"https://api.github.com/users/moonso/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-09-25T07:45:16Z","updated_at":"2015-09-25T15:50:43Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ewels/MultiQC/pulls/39","html_url":"https://github.com/ewels/MultiQC/pull/39","diff_url":"https://github.com/ewels/MultiQC/pull/39.diff","patch_url":"https://github.com/ewels/MultiQC/pull/39.patch"},"body":"- Updated cli, uses click\r\n- Moved code out of __init__ according to https://www.python.org/dev/peps/pep-0008/ (this should be done in the modules to, but that will be next pull request:)\r\n- Use proper loghandler in multiqc/log.py\r\n- import modules in __init__ instead of run script for more clean code"},"comment":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/comments/143259066","html_url":"https://github.com/ewels/MultiQC/pull/39#issuecomment-143259066","issue_url":"https://api.github.com/repos/ewels/MultiQC/issues/39","id":143259066,"user":{"login":"moonso","id":405278,"avatar_url":"https://avatars.githubusercontent.com/u/405278?v=3","gravatar_id":"","url":"https://api.github.com/users/moonso","html_url":"https://github.com/moonso","followers_url":"https://api.github.com/users/moonso/followers","following_url":"https://api.github.com/users/moonso/following{/other_user}","gists_url":"https://api.github.com/users/moonso/gists{/gist_id}","starred_url":"https://api.github.com/users/moonso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/moonso/subscriptions","organizations_url":"https://api.github.com/users/moonso/orgs","repos_url":"https://api.github.com/users/moonso/repos","events_url":"https://api.github.com/users/moonso/events{/privacy}","received_events_url":"https://api.github.com/users/moonso/received_events","type":"User","site_admin":false},"created_at":"2015-09-25T15:50:43Z","updated_at":"2015-09-25T15:50:43Z","body":"To-do list based on our conversation:\r\n\r\n- [ ] Remove [debugging print](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L39-L40) statements\r\n- [ ] Get the version of the package in the `__init__.py` (from the setup) rather than explicitly listing twice\r\n- [ ] Allow multiple analysis directories to be given (positional, not flag arguments)\r\n  - See [this](http://stackoverflow.com/questions/7588620/os-walk-multiple-directories-at-once)\r\n- [ ] Update the version code to be like [TACA](https://github.com/SciLifeLab/TACA/blob/master/taca/cli.py#L17)\r\n- [ ] Remove [commented out code](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L42-L62)\r\n- [ ] Better [docstring](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L118)\r\n- [ ] Import [this](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L119) at the top...?\r\n- [ ] Move [this](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L124-L128) into the `__init__.py` stuff.\r\n- [ ] Keep [this](https://github.com/ewels/MultiQC/blob/master/scripts/multiqc#L191) in, maybe with a comment to apologise\r\n- [ ] Avoid overwriting `module` variable name [here](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L197)\r\n- [ ] Try to avoid having multiple variables that are _almost_ the same thing. [This](https://github.com/moonso/MultiQC/blob/258a45d6f72a5d4278b6c4b326547d1e012cb668/scripts/multiqc#L84) is not ordered. We have `module`, `run_modules`, `avail_mods` and `module_submods` or something.\r\n- [ ] Delete all of the commented out code.\r\n\r\nHopefully not as bad as it looks!"}}