{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":135699757,"defaultBranch":"master","name":"Cassiopeia","ownerLogin":"YosefLab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-06-01T09:44:53.000Z","ownerAvatar":"https://github.com/avatars/u/13837262?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1717626294.0","currentOid":""},"activityList":{"items":[{"before":"6ac3f8d14e11555a7f526fdd0e842654b99d09af","after":"748a94df9e13c2fce8f1197244f21c020bc3472f","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-06-27T16:56:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"saving progress","shortMessageHtmlLink":"saving progress"}},{"before":null,"after":"6ac3f8d14e11555a7f526fdd0e842654b99d09af","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-06-05T22:24:54.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"implemented linear amplification simulator","shortMessageHtmlLink":"implemented linear amplification simulator"}},{"before":null,"after":"da10097f7fd6dfc4aebb4f394a20a94bd4adfa77","ref":"refs/heads/ccphylo-update","pushedAt":"2024-05-17T13:26:45.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"colganwi","name":"William Colgan","path":"/colganwi","primaryAvatarUrl":"https://github.com/avatars/u/12516135?s=80&v=4"},"commit":{"message":"CCPhylo branch lengths","shortMessageHtmlLink":"CCPhylo branch lengths"}},{"before":"fca94b2aeb22365117f81c0330c7c941155000c3","after":null,"ref":"refs/heads/ecdna-simulator","pushedAt":"2024-05-08T18:21:43.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"}},{"before":"41dbff8886c886dd1972347f05e29fe8b9a3f0fc","after":"78442c426f9548bffe8111b97aa23b2ef04b06ab","ref":"refs/heads/master","pushedAt":"2024-05-08T18:21:33.000Z","pushType":"pr_merge","commitsCount":43,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"Merge pull request #240 from YosefLab/ecdna-simulator\n\necDNA simulator","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2241134110\" data-permission-text=\"Title is private\" data-url=\"https://github.com/YosefLab/Cassiopeia/issues/240\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/YosefLab/Cassiopeia/pull/240/hovercard\" href=\"https://github.com/YosefLab/Cassiopeia/pull/240\">#240</a> from YosefLab/ecdna-simulator"}},{"before":"83009eb3c82e538cc0adb2827681b012ed004063","after":"fca94b2aeb22365117f81c0330c7c941155000c3","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-05-08T18:12:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"removed old unused code","shortMessageHtmlLink":"removed old unused code"}},{"before":"a351abdf5867b68243b87db8c309e815dfd0a08b","after":"83009eb3c82e538cc0adb2827681b012ed004063","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-05-08T18:10:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"updated docs","shortMessageHtmlLink":"updated docs"}},{"before":"283cdc79e9961db27ac5a699377c5a2a6a3cb139","after":"a351abdf5867b68243b87db8c309e815dfd0a08b","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-05-08T18:08:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"covered edge case where no birth scale is in initial tree","shortMessageHtmlLink":"covered edge case where no birth scale is in initial tree"}},{"before":"77fc89b06a740b8fad11961e6309befd3cc2274f","after":"283cdc79e9961db27ac5a699377c5a2a6a3cb139","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-05-08T17:56:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"updated formatting issues and docs in birthdeathfitnessimulator","shortMessageHtmlLink":"updated formatting issues and docs in birthdeathfitnessimulator"}},{"before":"10621c04c63c5320fb28ba5cdf3c22f1dd691eb8","after":"77fc89b06a740b8fad11961e6309befd3cc2274f","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-15T23:26:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"updated notebooks","shortMessageHtmlLink":"updated notebooks"}},{"before":"b6cb41c7135d0f48ee11f48a2f3925a03c13c558","after":"10621c04c63c5320fb28ba5cdf3c22f1dd691eb8","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-15T23:16:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"updated notebooks","shortMessageHtmlLink":"updated notebooks"}},{"before":"4ef1270426580ddff7066ba7fff3c1877123e4e6","after":"b6cb41c7135d0f48ee11f48a2f3925a03c13c558","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-14T00:43:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"added ecDNA notebook","shortMessageHtmlLink":"added ecDNA notebook"}},{"before":"bffa6c00ec35b28145fe4a82825298728c071688","after":"4ef1270426580ddff7066ba7fff3c1877123e4e6","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-14T00:38:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"added ecDNA notebook","shortMessageHtmlLink":"added ecDNA notebook"}},{"before":"189538e38a30618f9aad2692ffe5ee15b1e3a3c0","after":"bffa6c00ec35b28145fe4a82825298728c071688","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-14T00:31:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"added ecDNA simulator to user guide","shortMessageHtmlLink":"added ecDNA simulator to user guide"}},{"before":"30b455251e89d1ad241224289be8ea259669afed","after":"189538e38a30618f9aad2692ffe5ee15b1e3a3c0","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-14T00:18:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"added ecDNA simulator to user guide","shortMessageHtmlLink":"added ecDNA simulator to user guide"}},{"before":"8bbcd1029b0c8f36aaf867df6df18b845c85d7d1","after":"30b455251e89d1ad241224289be8ea259669afed","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-14T00:10:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"rebuilding docs","shortMessageHtmlLink":"rebuilding docs"}},{"before":"7d63c8ea90d285c63bc3acedfc5dc32a3f440a89","after":"8bbcd1029b0c8f36aaf867df6df18b845c85d7d1","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-13T23:57:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"moved ecDNA simulator back to PriorityQueue","shortMessageHtmlLink":"moved ecDNA simulator back to PriorityQueue"}},{"before":"a476f12d27f1b7c33d5eccfb2f19cb88ee92bf93","after":"7d63c8ea90d285c63bc3acedfc5dc32a3f440a89","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-13T22:27:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"reverted back to PriorityQueue","shortMessageHtmlLink":"reverted back to PriorityQueue"}},{"before":"f32bfe0f872b78ab5ebe384833540f55f95b5d38","after":"a476f12d27f1b7c33d5eccfb2f19cb88ee92bf93","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-13T22:04:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"fixed tests","shortMessageHtmlLink":"fixed tests"}},{"before":"73f694e78fe401f8635fe422a925835a276df77c","after":"f32bfe0f872b78ab5ebe384833540f55f95b5d38","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-12T21:12:28.000Z","pushType":"push","commitsCount":31,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"updated format","shortMessageHtmlLink":"updated format"}},{"before":"5ceb883ebbec554687833fe7f449bca5b45a3e2e","after":"73f694e78fe401f8635fe422a925835a276df77c","ref":"refs/heads/ecdna-simulator","pushedAt":"2024-04-12T21:09:07.000Z","pushType":"push","commitsCount":202,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"cleanup","shortMessageHtmlLink":"cleanup"}},{"before":"1a7c5ac5132386bad89c7b52a390831578894a3b","after":"9228c614f3bd28cf63b8c11b6e48d756a6a62743","ref":"refs/heads/doublet-detection","pushedAt":"2024-03-21T11:57:22.000Z","pushType":"push","commitsCount":32,"pusher":{"login":"colganwi","name":"William Colgan","path":"/colganwi","primaryAvatarUrl":"https://github.com/avatars/u/12516135?s=80&v=4"},"commit":{"message":"Merge branch 'master' into doublet-detection","shortMessageHtmlLink":"Merge branch 'master' into doublet-detection"}},{"before":"dced9533d0a796bd9d4c65a8c44ecc726ec6dd65","after":null,"ref":"refs/heads/lca-reconstruct","pushedAt":"2024-03-08T15:47:03.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"colganwi","name":"William Colgan","path":"/colganwi","primaryAvatarUrl":"https://github.com/avatars/u/12516135?s=80&v=4"}},{"before":"bb2fd4f579bb14c1618460891d3a0ef5eea40fb3","after":"41dbff8886c886dd1972347f05e29fe8b9a3f0fc","ref":"refs/heads/master","pushedAt":"2024-03-08T15:46:52.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"colganwi","name":"William Colgan","path":"/colganwi","primaryAvatarUrl":"https://github.com/avatars/u/12516135?s=80&v=4"},"commit":{"message":"Merge pull request #238 from YosefLab/lca-reconstruct\n\nLca reconstruct","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2174858268\" data-permission-text=\"Title is private\" data-url=\"https://github.com/YosefLab/Cassiopeia/issues/238\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/YosefLab/Cassiopeia/pull/238/hovercard\" href=\"https://github.com/YosefLab/Cassiopeia/pull/238\">#238</a> from YosefLab/lca-reconstruct"}},{"before":"faf7467ce9000f2435a7ee8efab05a5c51beb184","after":"dced9533d0a796bd9d4c65a8c44ecc726ec6dd65","ref":"refs/heads/lca-reconstruct","pushedAt":"2024-03-07T21:45:58.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"reformatted","shortMessageHtmlLink":"reformatted"}},{"before":null,"after":"faf7467ce9000f2435a7ee8efab05a5c51beb184","ref":"refs/heads/lca-reconstruct","pushedAt":"2024-03-07T21:44:32.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mattjones315","name":"Matt Jones","path":"/mattjones315","primaryAvatarUrl":"https://github.com/avatars/u/9790110?s=80&v=4"},"commit":{"message":"fixed bug in lca-reconstruct of ambiguous states","shortMessageHtmlLink":"fixed bug in lca-reconstruct of ambiguous states"}},{"before":"35aebf8dcf7116ad436561371bb8eeaa9f65beac","after":"24fdc569b97440e7e0433d3337da966a06fa5728","ref":"refs/heads/branch-length-estimation-paper","pushedAt":"2024-02-23T07:53:47.000Z","pushType":"push","commitsCount":26,"pusher":{"login":"sprillo","name":"Sebastián Prillo","path":"/sprillo","primaryAvatarUrl":"https://github.com/avatars/u/10426884?s=80&v=4"},"commit":{"message":"Merge branch 'master' into branch-length-estimation-paper","shortMessageHtmlLink":"Merge branch 'master' into branch-length-estimation-paper"}},{"before":"02d1052c8eb4238bdb3dc727e943fceacbda98aa","after":"35aebf8dcf7116ad436561371bb8eeaa9f65beac","ref":"refs/heads/branch-length-estimation-paper","pushedAt":"2024-02-23T01:07:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sprillo","name":"Sebastián Prillo","path":"/sprillo","primaryAvatarUrl":"https://github.com/avatars/u/10426884?s=80&v=4"},"commit":{"message":"Fix undefined self.number_of_states from previous commit e739630","shortMessageHtmlLink":"Fix undefined self.number_of_states from previous commit <a class=\"commit-link\" data-hovercard-type=\"commit\" data-hovercard-url=\"https://github.com/YosefLab/Cassiopeia/commit/e739630b7a19ae46601a6dd724d42b67a6ed8a73/hovercard\" href=\"https://github.com/YosefLab/Cassiopeia/commit/e739630b7a19ae46601a6dd724d42b67a6ed8a73\"><tt>e739630</tt></a>"}},{"before":"ccbf91ce89841cd7e128e63b143cb409de7be5f0","after":"02d1052c8eb4238bdb3dc727e943fceacbda98aa","ref":"refs/heads/branch-length-estimation-paper","pushedAt":"2024-02-23T00:17:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sprillo","name":"Sebastián Prillo","path":"/sprillo","primaryAvatarUrl":"https://github.com/avatars/u/10426884?s=80&v=4"},"commit":{"message":"Upgraded ray version means we need ray.tune.search instead of ray.tune.suggest","shortMessageHtmlLink":"Upgraded ray version means we need ray.tune.search instead of ray.tun…"}},{"before":"a0ceb945b1c350397b32afe303cbb647d6f837c9","after":"ccbf91ce89841cd7e128e63b143cb409de7be5f0","ref":"refs/heads/branch-length-estimation-paper","pushedAt":"2024-02-22T23:49:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sprillo","name":"Sebastián Prillo","path":"/sprillo","primaryAvatarUrl":"https://github.com/avatars/u/10426884?s=80&v=4"},"commit":{"message":"Add new method add_root_edge_if_not_present for computing more accurate parsimonies under CRISPR/Cas9 model","shortMessageHtmlLink":"Add new method add_root_edge_if_not_present for computing more accura…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEcRMROQA","startCursor":null,"endCursor":null}},"title":"Activity · YosefLab/Cassiopeia"}