{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/143","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/143/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/143/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/143/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/143","id":77563663,"number":143,"title":"Update scientific python stack","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-18T08:40:24Z","updated_at":"2015-05-18T12:53:48Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/143","html_url":"https://github.com/galaxyproject/tools-iuc/pull/143","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/143.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/143.patch"},"body":"This PR changes the way we distribute python packages in a substantial way. Testing and comments really appreciated.\r\n\r\n* all python packages are now depending on one specific python version (2.7 in this case) using the `setup_python_environment`\r\n* all `packages` have the python version in it's package name `_python_2_7_`\r\n* packages based on python 3.4 can be created now\r\n* you **can not** mix old python installations with the new `setup_python_environment` ones\r\n\r\n@peterjc I have included a `reportlab` package, which can be used for biopython if you want to switch over to `setup_python_environment` for biopython as well\r\n\r\nI think this makes installing packages easier and more consistent with the way we install R libraries and enables us to finally have python2 and python3 coexisting in the TS. Any objections?\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/103050803","html_url":"https://github.com/galaxyproject/tools-iuc/pull/143#issuecomment-103050803","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/143","id":103050803,"user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"created_at":"2015-05-18T12:53:48Z","updated_at":"2015-05-18T12:53:48Z","body":"> This sounds good in principle - when tool authors using these Python 2.7 or 3.4 (or later 3.5 etc) dependencies should best practice be to use ``<command interpreter=\"python2.7\">`` or ``<command interpreter=\"python3.4\">`` to match? [This is future proof for Python 3.5 etc]\r\n\r\nI don't think this is necessary. As soon as you require the package your default python will be the one you imported. \r\n\r\n> I presume given names like ``package_python_2_7_reportlab_3_1_44`` this would imply a future ``package_python_3_4_reportlab_3_1_44`` to match?\r\n\r\nYes, this is the idea.\r\n\r\n> Assuming this goes in, I have no problem with us updating the Biopython packages. Would we keep ``package_biopython_1_65`` to mean Python 2 implicitly and add ``package_python_3_4_biopython_1_65``?\r\n\r\nI would keep `package_biopython_1_65` as it is. It's the one with the old installation method and the new one should have the `_python_2_7_` included, indicating the new method.\r\n"}}