{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":797369120,"defaultBranch":"main","name":"malco","ownerLogin":"monarch-initiative","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2024-05-07T17:38:45.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/5161984?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1725536266.0","currentOid":""},"activityList":{"items":[{"before":"022b9a37b84706f15702e6d13366c50a275f7359","after":"43cb5cc5fb5bd605983b149176a2056b770e5473","ref":"refs/heads/short_letter","pushedAt":"2024-09-27T17:44:51.000Z","pushType":"push","commitsCount":12,"pusher":{"login":"justaddcoffee","name":"Justin Reese","path":"/justaddcoffee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/150311?s=80&v=4"},"commit":{"message":"Add comment about how to create mondo collection using curategpt","shortMessageHtmlLink":"Add comment about how to create mondo collection using curategpt"}},{"before":"ec56a24a35f2a6598785256b3de73a94d51e481f","after":"7e90dd8781a3e1af03e3d6b5df8f3e73d7a7a9b3","ref":"refs/heads/main","pushedAt":"2024-09-24T18:05:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"analysis, add boxplot, try subcategory of hereditary diseases","shortMessageHtmlLink":"analysis, add boxplot, try subcategory of hereditary diseases"}},{"before":"5bb9ab5112718d185ed2f1a715ebaf4bde2a2436","after":"ec56a24a35f2a6598785256b3de73a94d51e481f","ref":"refs/heads/main","pushedAt":"2024-09-23T15:41:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added plot of inverse rank vs date, still messy","shortMessageHtmlLink":"added plot of inverse rank vs date, still messy"}},{"before":"57b562659e77478340b2c1b27647de41ec3be9dc","after":"022b9a37b84706f15702e6d13366c50a275f7359","ref":"refs/heads/short_letter","pushedAt":"2024-09-22T21:24:29.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"justaddcoffee","name":"Justin Reese","path":"/justaddcoffee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/150311?s=80&v=4"},"commit":{"message":"Add plots comparing the models","shortMessageHtmlLink":"Add plots comparing the models"}},{"before":"739f346901ea57695881d57833f74820f2dca8b6","after":"57b562659e77478340b2c1b27647de41ec3be9dc","ref":"refs/heads/short_letter","pushedAt":"2024-09-20T12:55:26.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"justaddcoffee","name":"Justin Reese","path":"/justaddcoffee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/150311?s=80&v=4"},"commit":{"message":"Merge branch 'short_letter' of https://github.com/monarch-initiative/malco into short_letter","shortMessageHtmlLink":"Merge branch 'short_letter' of https://github.com/monarch-initiative/…"}},{"before":"96aba297bebea8b07a6677203a33f40d660382a2","after":"5bb9ab5112718d185ed2f1a715ebaf4bde2a2436","ref":"refs/heads/main","pushedAt":"2024-09-18T19:15:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"corrected tox.ini to ignore analysis dir","shortMessageHtmlLink":"corrected tox.ini to ignore analysis dir"}},{"before":"98e05b7339d3caa14f7dcfb7f8079b2dfa6cf0d5","after":"96aba297bebea8b07a6677203a33f40d660382a2","ref":"refs/heads/main","pushedAt":"2024-09-18T18:41:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"forgot to rm a line","shortMessageHtmlLink":"forgot to rm a line"}},{"before":"653291d119a5fffb31b2779b8a52221dadfea50e","after":"98e05b7339d3caa14f7dcfb7f8079b2dfa6cf0d5","ref":"refs/heads/main","pushedAt":"2024-09-18T18:36:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"clean up, comments, edit make","shortMessageHtmlLink":"clean up, comments, edit make"}},{"before":"7e13e4b99a673958bc9c045924b7e9ed931ab30f","after":"653291d119a5fffb31b2779b8a52221dadfea50e","ref":"refs/heads/main","pushedAt":"2024-09-18T12:08:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"adding poetry lock because #66 gave: pyproject.toml changed significantly since poetry.lock was last generated. Run poetry lock [--no-update] to fix the lock file.","shortMessageHtmlLink":"adding poetry lock because #66 gave: pyproject.toml changed significa…"}},{"before":"04730bc62c5d711294dc0135ed2d4ed7b65762b0","after":"7e13e4b99a673958bc9c045924b7e9ed931ab30f","ref":"refs/heads/main","pushedAt":"2024-09-17T15:17:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"delete duplicated code for mult lang and model","shortMessageHtmlLink":"delete duplicated code for mult lang and model"}},{"before":"76e0fb3cc750ab89676be7a3f1735744acaf7689","after":"04730bc62c5d711294dc0135ed2d4ed7b65762b0","ref":"refs/heads/main","pushedAt":"2024-09-15T18:40:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added comments in analysis and added ita prompts without eng reply request","shortMessageHtmlLink":"added comments in analysis and added ita prompts without eng reply re…"}},{"before":"1e70ff6ea138000d369638965c9cf30099f6f266","after":"76e0fb3cc750ab89676be7a3f1735744acaf7689","ref":"refs/heads/main","pushedAt":"2024-09-10T12:17:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added missing file to previous commit and checked in cache for OMIM2MONDO","shortMessageHtmlLink":"added missing file to previous commit and checked in cache for OMIM2M…"}},{"before":"ef2e9c2b5fefe5d21a0a3c940f47690fdf17b76a","after":"1e70ff6ea138000d369638965c9cf30099f6f266","ref":"refs/heads/main","pushedAt":"2024-09-06T15:56:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"started working on analysis of found vs not found diseases, very rough","shortMessageHtmlLink":"started working on analysis of found vs not found diseases, very rough"}},{"before":"2913dc7210ca94c453572ec2ea46af08aa6bf6fa","after":"ef2e9c2b5fefe5d21a0a3c940f47690fdf17b76a","ref":"refs/heads/main","pushedAt":"2024-09-05T12:17:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"pull analysis file from short letter and rm file checked in by accident","shortMessageHtmlLink":"pull analysis file from short letter and rm file checked in by accident"}},{"before":"b697b076a0e7685388cb2a18c098f16bcc8b62f2","after":null,"ref":"refs/heads/modularize_io","pushedAt":"2024-09-05T11:37:46.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"}},{"before":"1b0a2317a853e57c70b7afd712b3a3de2bab08e0","after":null,"ref":"refs/heads/persist_cache","pushedAt":"2024-09-05T11:37:27.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"}},{"before":"f5cba0911b81cc397270c0685b75875a73b7a0ea","after":null,"ref":"refs/heads/differential_category","pushedAt":"2024-09-05T11:37:05.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"}},{"before":"ac4aba0afe6e1732bd1fe7e8a4934e8acc2de08c","after":null,"ref":"refs/heads/mult_models","pushedAt":"2024-09-05T11:36:44.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"}},{"before":"070f74c9c9e4d12e38b23942db97527d5e14b0c8","after":"2913dc7210ca94c453572ec2ea46af08aa6bf6fa","ref":"refs/heads/main","pushedAt":"2024-09-04T10:26:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"Moved cache files, tested it, minor cleanups","shortMessageHtmlLink":"Moved cache files, tested it, minor cleanups"}},{"before":"5c3ca68ef0bb12da2bf3cccbdaf9a3500a293b39","after":"070f74c9c9e4d12e38b23942db97527d5e14b0c8","ref":"refs/heads/main","pushedAt":"2024-09-03T17:55:34.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"Modularize io (#47)\n\n* if run step is manually aborted it can be restarted without recomputing what has already been computed. Needs more testing and works only if post_process has not started yet, but seems to do the tick\r\n\r\n* added somewhat dangerous cleanup, does the job but make it safer\r\n\r\n* finished modularization in theory: only not run ppkts are run, ontogpt output is appended, the full dataframe save location has been moved, plots and data dir spearated. BUT all of this needs to be tested\r\n\r\n* lifted buggy is_file(), tested adding a model, then adding a phenopacket, in both cases successful run\r\n\r\n* added possibility of ppkts not being correctly run. If output file is present but empty, rerun it. Tested.\r\n\r\n* significant cleanup of run with Daniel and Peter, input is now manually given thru csv file, extended analysis significantly\r\n\r\n* added safe saving of dfs and some analysis scripts","shortMessageHtmlLink":"Modularize io (#47)"}},{"before":"90a284a92ae9b550fb2a4525ae63866b4cb96cf8","after":"b697b076a0e7685388cb2a18c098f16bcc8b62f2","ref":"refs/heads/modularize_io","pushedAt":"2024-09-03T17:50:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added safe saving of dfs and some analysis scripts","shortMessageHtmlLink":"added safe saving of dfs and some analysis scripts"}},{"before":"504c9c18412f11ed927ef7c71d07cb3e65938683","after":"90a284a92ae9b550fb2a4525ae63866b4cb96cf8","ref":"refs/heads/modularize_io","pushedAt":"2024-08-21T16:27:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"significant cleanup of run with Daniel and Peter, input is now manually given thru csv file, extended analysis significantly","shortMessageHtmlLink":"significant cleanup of run with Daniel and Peter, input is now manual…"}},{"before":"c4cd4c6343ff17810d93a1aec991fa4c718091cc","after":"504c9c18412f11ed927ef7c71d07cb3e65938683","ref":"refs/heads/modularize_io","pushedAt":"2024-08-20T16:17:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added possibility of ppkts not being correctly run. If output file is present but empty, rerun it. Tested.","shortMessageHtmlLink":"added possibility of ppkts not being correctly run. If output file is…"}},{"before":"390519731516fdfa619bcddb3f418675f56042e2","after":"c4cd4c6343ff17810d93a1aec991fa4c718091cc","ref":"refs/heads/modularize_io","pushedAt":"2024-08-20T15:31:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"lifted buggy is_file(), tested adding a model, then adding a phenopacket, in both cases successful run","shortMessageHtmlLink":"lifted buggy is_file(), tested adding a model, then adding a phenopac…"}},{"before":"f3fd3ff4f08e8ab73b3c0fcc9e858b14f2768f09","after":"390519731516fdfa619bcddb3f418675f56042e2","ref":"refs/heads/modularize_io","pushedAt":"2024-08-19T16:21:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"finished modularization in theory: only not run ppkts are run, ontogpt output is appended, the full dataframe save location has been moved, plots and data dir spearated. BUT all of this needs to be tested","shortMessageHtmlLink":"finished modularization in theory: only not run ppkts are run, ontogp…"}},{"before":"601ffca8a73af70e8345c85a882b280d8ff272f2","after":"f3fd3ff4f08e8ab73b3c0fcc9e858b14f2768f09","ref":"refs/heads/modularize_io","pushedAt":"2024-08-15T17:41:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"added somewhat dangerous cleanup, does the job but make it safer","shortMessageHtmlLink":"added somewhat dangerous cleanup, does the job but make it safer"}},{"before":null,"after":"601ffca8a73af70e8345c85a882b280d8ff272f2","ref":"refs/heads/modularize_io","pushedAt":"2024-08-15T17:38:06.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"if run step is manually aborted it can be restarted without recomputing what has already been computed. Needs more testing and works only if post_process has not started yet, but seems to do the tick","shortMessageHtmlLink":"if run step is manually aborted it can be restarted without recomputi…"}},{"before":"7c03bd2082e0feb02b0a75774c8561692bf12599","after":"5c3ca68ef0bb12da2bf3cccbdaf9a3500a293b39","ref":"refs/heads/main","pushedAt":"2024-08-15T16:34:58.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"Persist cache (#44)\n\n* fixed most issues\r\n\r\n* finished persisting cache","shortMessageHtmlLink":"Persist cache (#44)"}},{"before":"112bbe9ba711312f3f6329bef090faabecdd4fb6","after":"1b0a2317a853e57c70b7afd712b3a3de2bab08e0","ref":"refs/heads/persist_cache","pushedAt":"2024-08-15T16:33:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"finished persisting cache","shortMessageHtmlLink":"finished persisting cache"}},{"before":null,"after":"112bbe9ba711312f3f6329bef090faabecdd4fb6","ref":"refs/heads/persist_cache","pushedAt":"2024-08-14T16:14:24.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"leokim-l","name":null,"path":"/leokim-l","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/118829712?s=80&v=4"},"commit":{"message":"fixed most issues","shortMessageHtmlLink":"fixed most issues"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yN1QxNzo0NDo1MS4wMDAwMDBazwAAAATC4OQH","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0xNFQxNjoxNDoyNC4wMDAwMDBazwAAAASadGdD"}},"title":"Activity · monarch-initiative/malco"}