{"action":"created","issue":{"url":"https://api.github.com/repos/biojava/biojava/issues/245","labels_url":"https://api.github.com/repos/biojava/biojava/issues/245/labels{/name}","comments_url":"https://api.github.com/repos/biojava/biojava/issues/245/comments","events_url":"https://api.github.com/repos/biojava/biojava/issues/245/events","html_url":"https://github.com/biojava/biojava/issues/245","id":55608940,"number":245,"title":"Please vote: Major refactoring of package names (2nd attempt)","user":{"login":"josemduarte","id":6000474,"avatar_url":"https://avatars.githubusercontent.com/u/6000474?v=3","gravatar_id":"","url":"https://api.github.com/users/josemduarte","html_url":"https://github.com/josemduarte","followers_url":"https://api.github.com/users/josemduarte/followers","following_url":"https://api.github.com/users/josemduarte/following{/other_user}","gists_url":"https://api.github.com/users/josemduarte/gists{/gist_id}","starred_url":"https://api.github.com/users/josemduarte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josemduarte/subscriptions","organizations_url":"https://api.github.com/users/josemduarte/orgs","repos_url":"https://api.github.com/users/josemduarte/repos","events_url":"https://api.github.com/users/josemduarte/events{/privacy}","received_events_url":"https://api.github.com/users/josemduarte/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/biojava/biojava/labels/question","name":"question","color":"cc317c"},{"url":"https://api.github.com/repos/biojava/biojava/labels/urgent","name":"urgent","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/biojava/biojava/milestones/3","labels_url":"https://api.github.com/repos/biojava/biojava/milestones/3/labels","id":766290,"number":3,"title":"BioJava 4.0.0","description":"","creator":{"login":"sbliven","id":595872,"avatar_url":"https://avatars.githubusercontent.com/u/595872?v=3","gravatar_id":"","url":"https://api.github.com/users/sbliven","html_url":"https://github.com/sbliven","followers_url":"https://api.github.com/users/sbliven/followers","following_url":"https://api.github.com/users/sbliven/following{/other_user}","gists_url":"https://api.github.com/users/sbliven/gists{/gist_id}","starred_url":"https://api.github.com/users/sbliven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sbliven/subscriptions","organizations_url":"https://api.github.com/users/sbliven/orgs","repos_url":"https://api.github.com/users/sbliven/repos","events_url":"https://api.github.com/users/sbliven/events{/privacy}","received_events_url":"https://api.github.com/users/sbliven/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":21,"state":"open","created_at":"2014-08-26T16:32:25Z","updated_at":"2015-01-28T10:06:47Z","due_on":"2015-01-31T08:00:00Z","closed_at":null},"comments":15,"created_at":"2015-01-27T11:58:13Z","updated_at":"2015-01-28T11:04:14Z","closed_at":null,"body":"See original vote in #240 . Now we are extending the vote to include all proposed solutions.\r\n\r\nPlease vote on one of these solutions. If you are happy with more than one of them, then write down all solutions you like sorted from most ideal to least ideal (e.g. 3, 2, 1), I think that can help taking a final decision.\r\n\r\n1. __Keep existing situation__: a mix of `org.biojava3.modulename.*` and `org.biojava.bio.structure.*` (in structure and structure-gui modules)\r\n\r\n2. __In structure/structure-gui modules rename `org.biojava3.*` to `org.biojava.bio.structure.*`__ so that all other modules are `org.biojava3.*` while structure/structure-gui are `org.biojava.bio.structure.*`, proposed by @dmyersturnbull \r\n\r\n3. __Rename `org.biojava.bio.structure.*` to `org.biojava3.structure`__ : i.e. keep the biojava3 naming but making the whole project consistently use the `org.biojava3.modulename.*` scheme\r\n\r\n4. __Rename all packages to `org.biojava.modulename.*`__ , original solution proposed by @andreasprlic. This has issues with transitivity, as [explained](http://mailman.open-bio.org/pipermail/biojava-dev/2014-October/007847.html) by @heuermh \r\n\r\n5. __Rename all packages to `org.biojava4.modulename.*`__ and do the same for every major release, proposed by @paolopavan \r\n\r\n6. __Rename all packages to a new namespace that was never used before, e.g. `org.biojavax.modulename.*`__ : this avoids the transitivity issues and avoids renaming at every major release\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/biojava/biojava/issues/comments/71816446","html_url":"https://github.com/biojava/biojava/issues/245#issuecomment-71816446","issue_url":"https://api.github.com/repos/biojava/biojava/issues/245","id":71816446,"user":{"login":"paolopavan","id":1846955,"avatar_url":"https://avatars.githubusercontent.com/u/1846955?v=3","gravatar_id":"","url":"https://api.github.com/users/paolopavan","html_url":"https://github.com/paolopavan","followers_url":"https://api.github.com/users/paolopavan/followers","following_url":"https://api.github.com/users/paolopavan/following{/other_user}","gists_url":"https://api.github.com/users/paolopavan/gists{/gist_id}","starred_url":"https://api.github.com/users/paolopavan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolopavan/subscriptions","organizations_url":"https://api.github.com/users/paolopavan/orgs","repos_url":"https://api.github.com/users/paolopavan/repos","events_url":"https://api.github.com/users/paolopavan/events{/privacy}","received_events_url":"https://api.github.com/users/paolopavan/received_events","type":"User","site_admin":false},"created_at":"2015-01-28T11:04:14Z","updated_at":"2015-01-28T11:04:14Z","body":"There is one more important consideration that comes to me late. Biojava\r\ndistribution comes in modules which are currenlty named as biojava3-core,\r\nbiojava3-phylo and so on. Since they cross reference and can be downloaded\r\nseparately, I can see the need to keep them syncronized across major\r\nversion to avoid confusions and incompatibility.\r\nIt is better that this will be evident in the name and I see this one point\r\nin favour of 5. If not in the namespace, at least in jar name (that would\r\nanyway silently generate runtime errors in case of mismatch). Sorry\r\n@sbliven! :-)\r\n\r\nJust I want to remember that since we are talking about *major releases*,\r\nthey are *not* backward compatible by definition, as stated by semantic\r\nversioning. We should not try to make them so, it is a non sense, programs\r\nthat use biojava will fail at runtime for some unpredictable reasons. We\r\ncould at least try to import bug fixes in older versions if we want\r\nbackwards compatibility.\r\n\r\nDon't misunderstand me, this does not want to be any kind of harassment, it\r\nis just put some issues on the table and it is just my opinion, please\r\ncorrect me if I'm wrong.\r\nAnd I will stop bothering you now! :-D\r\n\r\n2015-01-28 11:06 GMT+01:00 Spencer Bliven <notifications@github.com>:\r\n\r\n> @andreasprlic <https://github.com/andreasprlic> #240\r\n> <https://github.com/biojava/biojava/issues/240> was inconclusive, and was\r\n> supplanted by this. I would really like to close this discussion now. No\r\n> one has voted for 1 (\"not now\") except as a final preference. I think the\r\n> 4.0.0 milestone is appropriate.\r\n>\r\n> —\r\n> Reply to this email directly or view it on GitHub\r\n> <https://github.com/biojava/biojava/issues/245#issuecomment-71809286>.\r\n>"}}