{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/638","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/638/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/638/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/638/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/638","id":119173565,"number":638,"title":"Remove duplicate code in util","user":{"login":"trendelkampschroer","id":5398411,"avatar_url":"https://avatars.githubusercontent.com/u/5398411?v=3","gravatar_id":"","url":"https://api.github.com/users/trendelkampschroer","html_url":"https://github.com/trendelkampschroer","followers_url":"https://api.github.com/users/trendelkampschroer/followers","following_url":"https://api.github.com/users/trendelkampschroer/following{/other_user}","gists_url":"https://api.github.com/users/trendelkampschroer/gists{/gist_id}","starred_url":"https://api.github.com/users/trendelkampschroer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/trendelkampschroer/subscriptions","organizations_url":"https://api.github.com/users/trendelkampschroer/orgs","repos_url":"https://api.github.com/users/trendelkampschroer/repos","events_url":"https://api.github.com/users/trendelkampschroer/events{/privacy}","received_events_url":"https://api.github.com/users/trendelkampschroer/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-11-27T10:38:46Z","updated_at":"2015-11-27T14:48:49Z","closed_at":null,"body":"There seems to be some duplicate code in \r\n\r\npyemma.util\r\n\r\nand \r\n\r\nmsmtools.util\r\n\r\nwe recently had to fix a bug in msmtools.util.statisics that needs to be copied over to pyemma. Would it be possible to move all submodules in pyemma.util that are also (partly) needed by msmtools to msmtools and import from msmtools in pyemma?\r\n\r\nTo be clear. I don't propose to completely move util from pyemma to msmtools. Both can have their own util modules. It would just be good to identify the functionality that is needed by msmtools and pyemma and have that residing in msmtools."},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/160153603","html_url":"https://github.com/markovmodel/PyEMMA/issues/638#issuecomment-160153603","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/638","id":160153603,"user":{"login":"franknoe","id":6495810,"avatar_url":"https://avatars.githubusercontent.com/u/6495810?v=3","gravatar_id":"","url":"https://api.github.com/users/franknoe","html_url":"https://github.com/franknoe","followers_url":"https://api.github.com/users/franknoe/followers","following_url":"https://api.github.com/users/franknoe/following{/other_user}","gists_url":"https://api.github.com/users/franknoe/gists{/gist_id}","starred_url":"https://api.github.com/users/franknoe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/franknoe/subscriptions","organizations_url":"https://api.github.com/users/franknoe/orgs","repos_url":"https://api.github.com/users/franknoe/repos","events_url":"https://api.github.com/users/franknoe/events{/privacy}","received_events_url":"https://api.github.com/users/franknoe/received_events","type":"User","site_admin":false},"created_at":"2015-11-27T14:48:49Z","updated_at":"2015-11-27T14:48:49Z","body":"OK, that sounds fine for me.\n\n> Am 27.11.2015 um 15:07 schrieb Frank Noe:\n>> True. The point was that this isn't really msmtools stuff, so it would\n>> rather be a separate package, but then we would need a converged API,\n>> but\n>> we keep changing things here. So I feel this would create many more\n>> headaches to introduce a dependency to another package at this point.\n>>\n> Honestly, why do we need a \"stable\" API for programmer/math/etc utilities?\n>\n> I'll suggest to create a repo only containing the util package at root\n> level, so we can include it via git subtrees in all dependent projects.\n>\n> A subtree is a merge of all the commits in a different repo into the\n> main repository under a given directory. This way we can easily share\n> the same code base for all projects using the util package.\n>\n> Further reading:\n> https://git-scm.com/book/en/v1/Git-Tools-Subtree-Merging\n>\n> This will actually not change the way we use util, but just the way we\n> maintain it (avoid copy paste code for instance).\n>\n> If desired, I can set this up.\n>\n>\n> ---\n> Reply to this email directly or view it on GitHub:\n> https://github.com/markovmodel/PyEMMA/issues/638#issuecomment-160148569\n\n\n"}}