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care of harmonizing the perl documentation:**\r\n- remove empty todo sections and empty bugs sections\r\n- harmonize /data/project/data/ to be /data/$PROJECT/data\r\n- harmonize authorship for the LORIS team\r\n- try to follow this pull request (#226) for the TODO section; i.e. use this: \"Fix comments written as #fixme in the code.\" whenever appropriate in other scripts\r\n- logHeader() function documented consistently (check #237 versus #246)\r\n- ensure that all tables and variables and paths to files are written in a C<> format \r\n- consistent INPUT vs INPUTS in Methods\r\n- consistency in the (constructor) method \r\n- INPUTS to functions when many inputs exist are now documented with (...), Nicolas raised this in this PR: #300; so PERHAPS reconsider revisiting all scripts to list all inputs anyway? (done)\r\n\r\nNote: the .md files are not created yet. Writing a script to automatically create perldoc becomes I don't feel doing it by hand (the script will be committed in a separate PR and could be run before each release so that if we forget to update a MD file in a PR, we can always mass run the creation of MD files) \r\n\r\nAssociated redmine ticket: https://redmine.cbrain.mcgill.ca/issues/13688 "},"comment":{"url":"https://api.github.com/repos/aces/Loris-MRI/issues/comments/399468986","html_url":"https://github.com/aces/Loris-MRI/pull/313#issuecomment-399468986","issue_url":"https://api.github.com/repos/aces/Loris-MRI/issues/313","id":399468986,"node_id":"MDEyOklzc3VlQ29tbWVudDM5OTQ2ODk4Ng==","user":{"login":"MounaSafiHarab","id":15198379,"node_id":"MDQ6VXNlcjE1MTk4Mzc5","avatar_url":"https://avatars1.githubusercontent.com/u/15198379?v=4","gravatar_id":"","url":"https://api.github.com/users/MounaSafiHarab","html_url":"https://github.com/MounaSafiHarab","followers_url":"https://api.github.com/users/MounaSafiHarab/followers","following_url":"https://api.github.com/users/MounaSafiHarab/following{/other_user}","gists_url":"https://api.github.com/users/MounaSafiHarab/gists{/gist_id}","starred_url":"https://api.github.com/users/MounaSafiHarab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MounaSafiHarab/subscriptions","organizations_url":"https://api.github.com/users/MounaSafiHarab/orgs","repos_url":"https://api.github.com/users/MounaSafiHarab/repos","events_url":"https://api.github.com/users/MounaSafiHarab/events{/privacy}","received_events_url":"https://api.github.com/users/MounaSafiHarab/received_events","type":"User","site_admin":false},"created_at":"2018-06-22T14:50:29Z","updated_at":"2018-06-22T14:50:29Z","author_association":"COLLABORATOR","body":"> @MounaSafiHarab I believe I addressed all your comments. Ready for testing.\r\n> \r\n> One question: do you want me to create the MD file before the merge or should I do it in a separate PR once this one is merged? Either is fine by me.\r\n\r\nI think we will use your newly created script in PR # to generate all the .md in the end (and fix any formatting issue we find then).\r\nFor now, I went over your changes and they all seem to be an improvement in consistency in the existing documentation, so it is definitely a step forwards and we can fix any little things we find as time goes by.\r\n\r\nI also checked out your branch and tested a couple of CCNA scans insertion, all went in, no issues at all, so I am ready to merge.\r\n\r\nOnly thing @cmadjar; this is going to minor and I do not want to ask you to rebase on 19.2 lol\r\n\r\n"}}
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