{"action":"created","issue":{"url":"https://api.github.com/repos/I2PC/scipion/issues/1616","repository_url":"https://api.github.com/repos/I2PC/scipion","labels_url":"https://api.github.com/repos/I2PC/scipion/issues/1616/labels{/name}","comments_url":"https://api.github.com/repos/I2PC/scipion/issues/1616/comments","events_url":"https://api.github.com/repos/I2PC/scipion/issues/1616/events","html_url":"https://github.com/I2PC/scipion/pull/1616","id":324874683,"number":1616,"title":"add eman2.21a to 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major release..","creator":{"login":"azazellochg","id":6952870,"avatar_url":"https://avatars3.githubusercontent.com/u/6952870?v=4","gravatar_id":"","url":"https://api.github.com/users/azazellochg","html_url":"https://github.com/azazellochg","followers_url":"https://api.github.com/users/azazellochg/followers","following_url":"https://api.github.com/users/azazellochg/following{/other_user}","gists_url":"https://api.github.com/users/azazellochg/gists{/gist_id}","starred_url":"https://api.github.com/users/azazellochg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/azazellochg/subscriptions","organizations_url":"https://api.github.com/users/azazellochg/orgs","repos_url":"https://api.github.com/users/azazellochg/repos","events_url":"https://api.github.com/users/azazellochg/events{/privacy}","received_events_url":"https://api.github.com/users/azazellochg/received_events","type":"User","site_admin":false},"open_issues":5,"closed_issues":1,"state":"open","created_at":"2018-04-10T13:16:44Z","updated_at":"2018-05-25T10:58:03Z","due_on":null,"closed_at":null},"comments":5,"created_at":"2018-05-21T10:59:18Z","updated_at":"2018-05-29T06:19:41Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/I2PC/scipion/pulls/1616","html_url":"https://github.com/I2PC/scipion/pull/1616","diff_url":"https://github.com/I2PC/scipion/pull/1616.diff","patch_url":"https://github.com/I2PC/scipion/pull/1616.patch"},"body":"This is a large PR, which comprises new Eman2 version support and a few things related to RCT protocols. I would like to request as many reviewers as possible since there are lots of changes. I am sorry that there is only one commit, but cherry picking from 1.2-based branch was not successfull due to too many differences between 1.2 and devel..\r\n\r\nGlobal changes:\r\n1) Eman2 updated to v2.21a, added EMAN2SCRATCHDIR var and mpi support to protocols\r\n2) constants.py file added combining all params from Eman protocols\r\n3) added readCTFModel func to read CTF from json files (xmipp cannot read hdf header yet)\r\n4) EMANMPIOPTS env var can be used by Scipion as SCIPION_MPI_FLAGS\r\n5) code formatting for all eman protocols, all of them are updated to support new EMAN2.21 options\r\n6) new test data for eman2 added (mostly for tilt validation test)\r\n\r\nBugfixes etc:\r\n1) writeSetOfParticles fixes: output files are named according to micName or micId\r\n2) e2converter write: propagate pix size, fixed wrong angle conversion for 2D/3D\r\n3) XmippProtExtractParticlesPairs has ctf options added\r\n4) added option to Eman refine easy to display html report\r\n5) This PR closes #766 and #1500\r\n\r\nNew protocols:\r\n1) ProtImportCoordinatesPairs to import tilt coord pairs from xmipp3 or eman2 (+test)\r\n2) Import ctf protocol now supports eman *json files\r\n3) EmanProtCTFAuto for e2ctf_auto.py in particles (with test and viewer)\r\n4) EmanProtRefine2D, EmanProtRefine2DBispec for 2D classification (with tests)\r\n5) EmanProtTiltValidate for e2tiltvalidate.py (with test and viewer)\r\n6) EmanProtAutopick for new fully automatic e2boxer.py\r\n7) EmanProtBoxing updated to run both old and new e2boxer.py in interactive mode\r\n\r\nNew tests:\r\n1. scipion test em.packages.eman2.tests.test_protocols_eman.TestEmanTiltValidate\r\n2. scipion test em.packages.eman2.tests.test_protocols_eman.TestEmanRefine2DBispec\r\n3. scipion test em.packages.eman2.tests.test_protocols_eman.TestEmanRefine2D\r\n4. scipion test em.packages.eman2.tests.test_protocols_eman.TestEmanCtfAuto\r\n5. scipion test tests.em.protocols.test_protocols_import_coords.TestImportCoordinatesPairs\r\n\r\nNew test data (unpack into data/tests/eman) - might be partially on the server already:\r\n[50Mb](https://mega.nz/#!F4wjXJBT!k9FMtTiemc3vh8ltRd1TmIp-NV9s7QzgNVxCDDa8Tro)\r\n\r\nNew eman2 tgz to upload to server: [440Mb](https://mega.nz/#!wspyCTSR!-8M5B9hU9dcfufd2_Lbal31YHJ20cKcc_UF4zGn2pRg)\r\n\r\nRemaining todo list:\r\n- [x] fix new eman installation\r\n- [ ] import particle set (lst) from Eman\r\n- [x] test for EmanProtAutopick\r\n\r\nPS. I tested it as much as possible with eman-2.12 and 2.21a, but that was only me :)\r\nPablo and Jose, you both have write permissions to push to my branch in this PR."},"comment":{"url":"https://api.github.com/repos/I2PC/scipion/issues/comments/392664667","html_url":"https://github.com/I2PC/scipion/pull/1616#issuecomment-392664667","issue_url":"https://api.github.com/repos/I2PC/scipion/issues/1616","id":392664667,"user":{"login":"pconesa","id":785633,"avatar_url":"https://avatars2.githubusercontent.com/u/785633?v=4","gravatar_id":"","url":"https://api.github.com/users/pconesa","html_url":"https://github.com/pconesa","followers_url":"https://api.github.com/users/pconesa/followers","following_url":"https://api.github.com/users/pconesa/following{/other_user}","gists_url":"https://api.github.com/users/pconesa/gists{/gist_id}","starred_url":"https://api.github.com/users/pconesa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pconesa/subscriptions","organizations_url":"https://api.github.com/users/pconesa/orgs","repos_url":"https://api.github.com/users/pconesa/repos","events_url":"https://api.github.com/users/pconesa/events{/privacy}","received_events_url":"https://api.github.com/users/pconesa/received_events","type":"User","site_admin":false},"created_at":"2018-05-29T06:19:40Z","updated_at":"2018-05-29T06:19:40Z","author_association":"MEMBER","body":"I must apologize for not putting the files on the server, sorry @azazellochg and the rest. Now they are ready."}}
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