{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/1996","repository_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/1996/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/1996/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/1996/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/pull/1996","id":350182847,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA4MDk1MDg0","number":1996,"title":"First pass at also supporting pip installations","user":{"login":"zougloub","id":998040,"node_id":"MDQ6VXNlcjk5ODA0MA==","avatar_url":"https://avatars1.githubusercontent.com/u/998040?v=4","gravatar_id":"","url":"https://api.github.com/users/zougloub","html_url":"https://github.com/zougloub","followers_url":"https://api.github.com/users/zougloub/followers","following_url":"https://api.github.com/users/zougloub/following{/other_user}","gists_url":"https://api.github.com/users/zougloub/gists{/gist_id}","starred_url":"https://api.github.com/users/zougloub/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zougloub/subscriptions","organizations_url":"https://api.github.com/users/zougloub/orgs","repos_url":"https://api.github.com/users/zougloub/repos","events_url":"https://api.github.com/users/zougloub/events{/privacy}","received_events_url":"https://api.github.com/users/zougloub/received_events","type":"User","site_admin":false},"labels":[{"id":137139873,"node_id":"MDU6TGFiZWwxMzcxMzk4NzM=","url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/feature","name":"feature","color":"5319e7","default":false},{"id":105947385,"node_id":"MDU6TGFiZWwxMDU5NDczODU=","url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/installation","name":"installation","color":"5319e7","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-08-13T20:31:59Z","updated_at":"2018-09-07T21:50:19Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/pulls/1996","html_url":"https://github.com/neuropoly/spinalcordtoolbox/pull/1996","diff_url":"https://github.com/neuropoly/spinalcordtoolbox/pull/1996.diff","patch_url":"https://github.com/neuropoly/spinalcordtoolbox/pull/1996.patch"},"body":"Currently sct is officially installed using its installer, and all the tools are command-line tools, however we're working towards having a Python API, and in this case we'd really want to have SCT usable as any other Python library.\r\n\r\nThis PR will add basic pip setup-ability and keep the \"installer way\" functional.\r\n\r\nFor now, we're talking about being able to do something as simple as:\r\n\r\n```sh\r\ngit clone https://github.com/neuropoly/spinalcordtoolbox\r\ncd spinalcordtoolbox\r\npip install -e .\r\nsct_testing\r\n```\r\n\r\nAnd to be able to do:\r\n\r\n```python\r\n>>> from spinalcordtoolbox.image import Image\r\n```\r\n\r\nand use the Python API, typically in Jupyter notebooks.\r\n\r\nThe strategy:\r\n\r\n- [x] When using the installer, reuse the pip installation (will make the installer slimmer)\r\n- [x] When using the installer, install fixed versions of dependencies with conda\r\n- [x] Except for special cases, dependencies expressed with setup.py will have no specific version required (so when installing after Conda install, they will be skipped as already there)\r\n- [x] Install command-line shims using `setup.py` `entry_points`\r\n- [x] Create a `spinalcordtoolbox.compat.launcher` module to launch the scripts\r\n- [x] Handle binaries installation\r\n- [ ] Handle data installation\r\n- [x] Handle MPI mode\r\n"},"comment":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/comments/419575046","html_url":"https://github.com/neuropoly/spinalcordtoolbox/pull/1996#issuecomment-419575046","issue_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/1996","id":419575046,"node_id":"MDEyOklzc3VlQ29tbWVudDQxOTU3NTA0Ng==","user":{"login":"jcohenadad","id":2482071,"node_id":"MDQ6VXNlcjI0ODIwNzE=","avatar_url":"https://avatars1.githubusercontent.com/u/2482071?v=4","gravatar_id":"","url":"https://api.github.com/users/jcohenadad","html_url":"https://github.com/jcohenadad","followers_url":"https://api.github.com/users/jcohenadad/followers","following_url":"https://api.github.com/users/jcohenadad/following{/other_user}","gists_url":"https://api.github.com/users/jcohenadad/gists{/gist_id}","starred_url":"https://api.github.com/users/jcohenadad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jcohenadad/subscriptions","organizations_url":"https://api.github.com/users/jcohenadad/orgs","repos_url":"https://api.github.com/users/jcohenadad/repos","events_url":"https://api.github.com/users/jcohenadad/events{/privacy}","received_events_url":"https://api.github.com/users/jcohenadad/received_events","type":"User","site_admin":false},"created_at":"2018-09-07T21:50:19Z","updated_at":"2018-09-07T21:50:19Z","author_association":"CONTRIBUTOR","body":"@zougloub i would in fact, because currently all new SCT installations (let's call it sct-new) would systematically install data under sct-new/data, and would append a new SCT_DIR to the `.bashrc`. But you already know that so i guess i don't understand your question :P"}}
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