{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":712578150,"defaultBranch":"main","name":"meet-the-neighbors","ownerLogin":"mcn3159","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-10-31T18:42:01.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/130867889?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1711145618.0","currentOid":""},"activityList":{"items":[{"before":"96b44412d1fb26e78d3aa426c6c2f8979432a985","after":"6cb3293f3d56c547ffefe456b70afc92a0a4175d","ref":"refs/heads/hotfix","pushedAt":"2024-07-02T15:39:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Grab cluster centroids of neighborhoods for gLM.","shortMessageHtmlLink":"Grab cluster centroids of neighborhoods for gLM."}},{"before":"8980f1e9fe1407439aa8515f77c3238e15341f77","after":"5fd51ca32a4a85ecb22b33ddd616b14e3de89120","ref":"refs/heads/dev","pushedAt":"2024-06-11T21:23:10.000Z","pushType":"pr_merge","commitsCount":5,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #19 from mcn3159/hotfix\n\nHotfix","shortMessageHtmlLink":"Merge pull request #19 from mcn3159/hotfix"}},{"before":"27d811926f225b57e4dab5a1cbfc2578ac83c0a1","after":"7e1de1256735ac55a3c2c8b1e0a8193c686ce91d","ref":"refs/heads/main","pushedAt":"2024-06-11T21:22:20.000Z","pushType":"pr_merge","commitsCount":26,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #18 from mcn3159/dev\n\nDev","shortMessageHtmlLink":"Merge pull request #18 from mcn3159/dev"}},{"before":"c2a01916e7898cb01a89bcfb0270ac17dd42a47d","after":"96b44412d1fb26e78d3aa426c6c2f8979432a985","ref":"refs/heads/hotfix","pushedAt":"2024-06-11T15:15:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add olp_window arg, ummaper.obj saves to outdir,","shortMessageHtmlLink":"Add olp_window arg, ummaper.obj saves to outdir,"}},{"before":"e9b8e8ceffc0178c6af1cbd115197106c80a8420","after":"c2a01916e7898cb01a89bcfb0270ac17dd42a47d","ref":"refs/heads/hotfix","pushedAt":"2024-06-11T15:14:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add args param to funcs\nCheck if prots extracted from neighbors meet minimum neighborhood requirements b/c partial/pseudo genes tend not to have a protein","shortMessageHtmlLink":"Add args param to funcs"}},{"before":"be336cd3c0f6e0e2a53dfbfca1f1dc99ae6de41d","after":"e9b8e8ceffc0178c6af1cbd115197106c80a8420","ref":"refs/heads/hotfix","pushedAt":"2024-06-11T15:06:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Prevent error by attempting resaving of embed_df","shortMessageHtmlLink":"Prevent error by attempting resaving of embed_df"}},{"before":"294dac47c3d1b3ad900315c38dd48614841c1e4f","after":"be336cd3c0f6e0e2a53dfbfca1f1dc99ae6de41d","ref":"refs/heads/hotfix","pushedAt":"2024-05-17T19:50:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Fix some bugs in compute_umap, not all","shortMessageHtmlLink":"Fix some bugs in compute_umap, not all"}},{"before":"58a880f325545f88fded63eb11f9c38daac33ac2","after":"8980f1e9fe1407439aa8515f77c3238e15341f77","ref":"refs/heads/dev","pushedAt":"2024-05-10T19:41:48.000Z","pushType":"pr_merge","commitsCount":5,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #17 from mcn3159/hotfix\n\nHotfix with big feature updates","shortMessageHtmlLink":"Merge pull request #17 from mcn3159/hotfix"}},{"before":"5e6a90c34c81f0a071667e39263f60885b625bee","after":"294dac47c3d1b3ad900315c38dd48614841c1e4f","ref":"refs/heads/hotfix","pushedAt":"2024-05-10T19:36:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Speed up neighborhood object calling","shortMessageHtmlLink":"Speed up neighborhood object calling"}},{"before":"f229546e02cdb09bf8f9ca364e9a0b34812b7d9d","after":"17906c8eaa1968a5067a0a5fcc794b1d679e4133","ref":"refs/heads/patch","pushedAt":"2024-04-30T22:13:12.000Z","pushType":"pr_merge","commitsCount":22,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #16 from mcn3159/hotfix\n\nHotfix","shortMessageHtmlLink":"Merge pull request #16 from mcn3159/hotfix"}},{"before":"bf1200a819d1d5c32eb387ef6370f1d6174a40a5","after":"f229546e02cdb09bf8f9ca364e9a0b34812b7d9d","ref":"refs/heads/patch","pushedAt":"2024-04-30T22:11:52.000Z","pushType":"pr_merge","commitsCount":9,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #15 from mcn3159/main\n\nCatch up with main","shortMessageHtmlLink":"Merge pull request #15 from mcn3159/main"}},{"before":"a39db60b1b73a1e4b41788acf66ef1c65317c6e1","after":"5e6a90c34c81f0a071667e39263f60885b625bee","ref":"refs/heads/hotfix","pushedAt":"2024-04-26T21:13:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add logger as parameter to map_vfs function","shortMessageHtmlLink":"Add logger as parameter to map_vfs function"}},{"before":"71c691abfae001576d7c067f2daa719bf21b1ff0","after":"a39db60b1b73a1e4b41788acf66ef1c65317c6e1","ref":"refs/heads/hotfix","pushedAt":"2024-04-26T21:04:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Implement logging","shortMessageHtmlLink":"Implement logging"}},{"before":"853ed198a1d41b4cb7e6b6b40d1838f56255ef74","after":"71c691abfae001576d7c067f2daa719bf21b1ff0","ref":"refs/heads/hotfix","pushedAt":"2024-04-25T15:33:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Overwrite combined_fasta_clust_reps.\nTo make sure gLM embeddings are same as mmseq_clust","shortMessageHtmlLink":"Overwrite combined_fasta_clust_reps."}},{"before":"bb690dfc79bf5d776e11eec62163f7221d28414c","after":"58a880f325545f88fded63eb11f9c38daac33ac2","ref":"refs/heads/dev","pushedAt":"2024-04-04T22:57:12.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #14 from mcn3159/hotfix\n\nHotfix","shortMessageHtmlLink":"Merge pull request #14 from mcn3159/hotfix"}},{"before":"4e14488b076018c641bff5d95a3621a0a5e7a97b","after":"853ed198a1d41b4cb7e6b6b40d1838f56255ef74","ref":"refs/heads/hotfix","pushedAt":"2024-04-04T22:56:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add comment to compute_umap\nMake --resume more efficient.\n-Check if mmseqs_clust*.tsv exists, instead of recomputing","shortMessageHtmlLink":"Add comment to compute_umap"}},{"before":"2da94d7713e651ab6a6f70aed543bf78803a64af","after":"4e14488b076018c641bff5d95a3621a0a5e7a97b","ref":"refs/heads/hotfix","pushedAt":"2024-04-02T21:23:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Change func() names and add comments for clarity.\nRemove search res resaving, use more mmseq_clust.\nRemove redundant genes in neighborhoods, by\nremoving duplicate start positions","shortMessageHtmlLink":"Change func() names and add comments for clarity."}},{"before":"0368ef6618f0d8b13184bdf40115d2bcecdb26ed","after":"bb690dfc79bf5d776e11eec62163f7221d28414c","ref":"refs/heads/dev","pushedAt":"2024-03-27T19:01:49.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #13 from mcn3159/hotfix\n\nHotfix","shortMessageHtmlLink":"Merge pull request #13 from mcn3159/hotfix"}},{"before":"df438d40d8d7ab60db9566296347e44720f10978","after":"2da94d7713e651ab6a6f70aed543bf78803a64af","ref":"refs/heads/hotfix","pushedAt":"2024-03-27T19:00:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Give and save umap obj and embedding df","shortMessageHtmlLink":"Give and save umap obj and embedding df"}},{"before":"953caecf550b3a6483a212dd8abc480d70c445ff","after":"df438d40d8d7ab60db9566296347e44720f10978","ref":"refs/heads/hotfix","pushedAt":"2024-03-27T16:25:19.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #12 from mcn3159/dev\n\nAdd vfdb categories to mmseqs clust","shortMessageHtmlLink":"Merge pull request #12 from mcn3159/dev"}},{"before":"b088309e7653299a2db52b5a5885887dcd84ea7b","after":"0368ef6618f0d8b13184bdf40115d2bcecdb26ed","ref":"refs/heads/dev","pushedAt":"2024-03-27T16:21:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add vfdb categories to mmseqs clust","shortMessageHtmlLink":"Add vfdb categories to mmseqs clust"}},{"before":"be2394411cca898ab2d3301bb243650bae59aaea","after":"953caecf550b3a6483a212dd8abc480d70c445ff","ref":"refs/heads/hotfix","pushedAt":"2024-03-27T16:19:55.000Z","pushType":"pr_merge","commitsCount":9,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #11 from mcn3159/dev\n\nDev","shortMessageHtmlLink":"Merge pull request #11 from mcn3159/dev"}},{"before":"00ee3d30bc392c05578232c90e883e36ecfc7065","after":"b088309e7653299a2db52b5a5885887dcd84ea7b","ref":"refs/heads/dev","pushedAt":"2024-03-26T18:39:53.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add tab separater when reading in mmseqs","shortMessageHtmlLink":"Add tab separater when reading in mmseqs"}},{"before":"51e649c365992e2619307f462160fea0bd3fd06d","after":"00ee3d30bc392c05578232c90e883e36ecfc7065","ref":"refs/heads/dev","pushedAt":"2024-03-22T22:13:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add files via upload\n\nCompute and save umaps from a given glm_output directory","shortMessageHtmlLink":"Add files via upload"}},{"before":"38a63cf420ae21c0b405d23596372199aa5e7ab3","after":"51e649c365992e2619307f462160fea0bd3fd06d","ref":"refs/heads/dev","pushedAt":"2024-03-22T22:02:59.000Z","pushType":"pr_merge","commitsCount":11,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #10 from mcn3159/hotfix\n\nHotfix","shortMessageHtmlLink":"Merge pull request #10 from mcn3159/hotfix"}},{"before":"bbd174d62e213c75b938a63fdc37a8dc7cd418d1","after":"be2394411cca898ab2d3301bb243650bae59aaea","ref":"refs/heads/hotfix","pushedAt":"2024-03-22T15:39:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"glm inputs should now include genus and species","shortMessageHtmlLink":"glm inputs should now include genus and species"}},{"before":"aac3c184bbe093c497c5e56e8ade47cf01f6cae8","after":"bbd174d62e213c75b938a63fdc37a8dc7cd418d1","ref":"refs/heads/hotfix","pushedAt":"2024-03-22T15:30:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add files via upload\n\nAdd vfdb species and genus to glm tsv inputs","shortMessageHtmlLink":"Add files via upload"}},{"before":"4b9582bcd67bc64b57a6f4944372f17957d3d9e2","after":"aac3c184bbe093c497c5e56e8ade47cf01f6cae8","ref":"refs/heads/hotfix","pushedAt":"2024-03-22T15:29:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Add files via upload\n\nAdd the species and genus of vfs from vfdb to mmseqs_clust df.","shortMessageHtmlLink":"Add files via upload"}},{"before":"f1ebc0e8a12a9065da654caff8bd3809bba91c3f","after":"4b9582bcd67bc64b57a6f4944372f17957d3d9e2","ref":"refs/heads/hotfix","pushedAt":"2024-03-22T15:25:01.000Z","pushType":"pr_merge","commitsCount":13,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"Merge pull request #9 from mcn3159/main\n\nBring up to speed with main","shortMessageHtmlLink":"Merge pull request #9 from mcn3159/main"}},{"before":"2be2c5178b80cbd7506023992dbaa031f9a16a55","after":"38a63cf420ae21c0b405d23596372199aa5e7ab3","ref":"refs/heads/dev","pushedAt":"2024-03-20T20:10:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mcn3159","name":null,"path":"/mcn3159","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/130867889?s=80&v=4"},"commit":{"message":"glm_input names are now only the query protein.","shortMessageHtmlLink":"glm_input names are now only the query protein."}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEdP4IZAA","startCursor":null,"endCursor":null}},"title":"Activity ยท mcn3159/meet-the-neighbors"}