{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":55709169,"defaultBranch":"master","name":"treetime","ownerLogin":"neherlab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2016-04-07T16:12:19.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/8996580?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1713778762.0","currentOid":""},"activityList":{"items":[{"before":"96ab18b4599c9917e2ea762829dfc90e9160a0ef","after":"d9ded2799b2a79400889c565f2e2ad62ecb889a4","ref":"refs/heads/feat/graph-biphasic-traversal","pushedAt":"2024-04-24T07:53:22.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"feat: reimpl fitch reconstruction based on concurrent biphasic traversal","shortMessageHtmlLink":"feat: reimpl fitch reconstruction based on concurrent biphasic traversal"}},{"before":"d57fda63d90c3c25ffb19eff4e0d948db5ab2272","after":"a31533b3e2744cb8078a7cb223535ef6d0369e6f","ref":"refs/heads/rust","pushedAt":"2024-04-24T07:53:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"chore: reduce noise in test output","shortMessageHtmlLink":"chore: reduce noise in test output"}},{"before":"47d5d46d1eb46234dfdb250ec204a05cc5d99ddc","after":"96ab18b4599c9917e2ea762829dfc90e9160a0ef","ref":"refs/heads/feat/graph-biphasic-traversal","pushedAt":"2024-04-23T05:42:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: ensure thread barrier between pre- and post- phases","shortMessageHtmlLink":"fix: ensure thread barrier between pre- and post- phases"}},{"before":null,"after":"47d5d46d1eb46234dfdb250ec204a05cc5d99ddc","ref":"refs/heads/feat/graph-biphasic-traversal","pushedAt":"2024-04-22T09:39:22.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"feat: add biphasic graph traversal","shortMessageHtmlLink":"feat: add biphasic graph traversal"}},{"before":"fe28b0ba8f688c9f3614ea5746e6c83237a33a74","after":"d904cb733167a8a719b4a1004df7dca84c25b639","ref":"refs/heads/tmp_py","pushedAt":"2024-04-17T16:47:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"remove sequences from node to temporary storage","shortMessageHtmlLink":"remove sequences from node to temporary storage"}},{"before":"b6ed162502975f911254fc7c375fd4beb3292974","after":"d57fda63d90c3c25ffb19eff4e0d948db5ab2272","ref":"refs/heads/rust","pushedAt":"2024-04-15T18:20:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: make states unique","shortMessageHtmlLink":"fix: make states unique"}},{"before":"b128eff42ea129082c01c01c85652521c855d745","after":"b6ed162502975f911254fc7c375fd4beb3292974","ref":"refs/heads/rust","pushedAt":"2024-04-15T18:14:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: order of iteration of child states in the zip","shortMessageHtmlLink":"fix: order of iteration of child states in the zip"}},{"before":"bee02fc14bafa0d793336623d371f9154026a333","after":"b128eff42ea129082c01c01c85652521c855d745","ref":"refs/heads/rust","pushedAt":"2024-04-15T17:27:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"refactor: port \"refactor: streamline fitch\"\n\nport of https://github.com/neherlab/treetime/commit/fe28b0ba8f688c9f3614ea5746e6c83237a33a74","shortMessageHtmlLink":"refactor: port \"refactor: streamline fitch\""}},{"before":"e51a42cdecec745f42ebdf35a5c04e9397f72ca2","after":"fe28b0ba8f688c9f3614ea5746e6c83237a33a74","ref":"refs/heads/tmp_py","pushedAt":"2024-04-15T09:03:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"refactor: streamline fitch","shortMessageHtmlLink":"refactor: streamline fitch"}},{"before":"e25cc13243e09378493893409468deedcb43ef80","after":"bee02fc14bafa0d793336623d371f9154026a333","ref":"refs/heads/rust","pushedAt":"2024-04-15T04:43:27.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: split fasta name and desc in the reader","shortMessageHtmlLink":"fix: split fasta name and desc in the reader"}},{"before":"3efcdba0c16c6fae6ebb6bc4fb6d9ac6a70dc2d1","after":"e25cc13243e09378493893409468deedcb43ef80","ref":"refs/heads/rust","pushedAt":"2024-04-15T04:42:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: split fasta name and desc in the reader","shortMessageHtmlLink":"fix: split fasta name and desc in the reader"}},{"before":"15e92207a7bedd350a56d7dd47206689bb1f1ce8","after":"3efcdba0c16c6fae6ebb6bc4fb6d9ac6a70dc2d1","ref":"refs/heads/rust","pushedAt":"2024-04-15T04:31:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: apply non-nuc changes only if leaf reconstruction is requested","shortMessageHtmlLink":"fix: apply non-nuc changes only if leaf reconstruction is requested"}},{"before":"8b1648578ad7cee9afad5b7e43fb3f4eeacfbeaa","after":"15e92207a7bedd350a56d7dd47206689bb1f1ce8","ref":"refs/heads/rust","pushedAt":"2024-04-15T04:13:13.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"perf: improve iteration over positions\n\nport of https://github.com/neherlab/treetime/commit/6e20d910386c42d3d9916aa894c92842e735556e","shortMessageHtmlLink":"perf: improve iteration over positions"}},{"before":"5eae8f31f43ccbc7952aad8872d3cf8afa5f9b65","after":"8b1648578ad7cee9afad5b7e43fb3f4eeacfbeaa","ref":"refs/heads/rust","pushedAt":"2024-04-15T04:08:13.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"perf: improve iteration over positions\n\nport of https://github.com/neherlab/treetime/commit/6e20d910386c42d3d9916aa894c92842e735556e","shortMessageHtmlLink":"perf: improve iteration over positions"}},{"before":"0c7e03a3b64beb15d9012a46501f18607ac05afc","after":"5eae8f31f43ccbc7952aad8872d3cf8afa5f9b65","ref":"refs/heads/rust","pushedAt":"2024-04-15T03:57:43.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"perf: improve iteration over positions\n\nport of https://github.com/neherlab/treetime/commit/6e20d910386c42d3d9916aa894c92842e735556e","shortMessageHtmlLink":"perf: improve iteration over positions"}},{"before":"6e20d910386c42d3d9916aa894c92842e735556e","after":"e51a42cdecec745f42ebdf35a5c04e9397f72ca2","ref":"refs/heads/tmp_py","pushedAt":"2024-04-14T17:06:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"add prototype of branch length optimization without canned optimization routines","shortMessageHtmlLink":"add prototype of branch length optimization without canned optimizati…"}},{"before":"6f110aa66b3e28c8224050950761b86ba7950d8f","after":"6e20d910386c42d3d9916aa894c92842e735556e","ref":"refs/heads/tmp_py","pushedAt":"2024-04-13T19:58:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"refactor: redo fitch state calculation","shortMessageHtmlLink":"refactor: redo fitch state calculation"}},{"before":"b7474344fcb96f5da5f5492914e36109b40c61e7","after":"0c7e03a3b64beb15d9012a46501f18607ac05afc","ref":"refs/heads/rust","pushedAt":"2024-04-13T00:33:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: apply non-nuc seq ranges only during reconstruction","shortMessageHtmlLink":"fix: apply non-nuc seq ranges only during reconstruction"}},{"before":"6291afb254aac41ac02be59f212fa38e13aad98f","after":"b7474344fcb96f5da5f5492914e36109b40c61e7","ref":"refs/heads/rust","pushedAt":"2024-04-13T00:20:40.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"refactor: reformat","shortMessageHtmlLink":"refactor: reformat"}},{"before":"428f6440f8994718844dbe229d993f5117fabdc3","after":"6291afb254aac41ac02be59f212fa38e13aad98f","ref":"refs/heads/rust","pushedAt":"2024-04-12T17:39:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"fix: catch if position doesn't exist in parent.profile_variable","shortMessageHtmlLink":"fix: catch if position doesn't exist in parent.profile_variable"}},{"before":"207b07806d507ab65ba0ec22d267b63747d7edd0","after":"428f6440f8994718844dbe229d993f5117fabdc3","ref":"refs/heads/rust","pushedAt":"2024-04-12T13:51:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"chore: delete empty file","shortMessageHtmlLink":"chore: delete empty file"}},{"before":"68474dd49eaa439388bbb427cadaa5c55cf8d18a","after":"207b07806d507ab65ba0ec22d267b63747d7edd0","ref":"refs/heads/rust","pushedAt":"2024-04-12T13:50:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"fix: use alphabet instead of hardcoded characters","shortMessageHtmlLink":"fix: use alphabet instead of hardcoded characters"}},{"before":"34f34b675c0afafefde216c0f589ea5545f0d9eb","after":"68474dd49eaa439388bbb427cadaa5c55cf8d18a","ref":"refs/heads/rust","pushedAt":"2024-04-12T11:32:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"chore: remove commented sequences","shortMessageHtmlLink":"chore: remove commented sequences"}},{"before":"fe4f702bd0f879c9cf73cdfd5341c233a2fb470a","after":null,"ref":"refs/heads/fix/rust_child_seq","pushedAt":"2024-04-12T11:29:02.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"}},{"before":"f9d95f215ff0b71f54726b6c7d2d1098405dba04","after":"34f34b675c0afafefde216c0f589ea5545f0d9eb","ref":"refs/heads/rust","pushedAt":"2024-04-12T11:28:38.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/fix/rust_child_seq' into rust","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/fix/rust_child_seq' into rust"}},{"before":"894e014c44c44657a6afff73b3fa2477a2fd31fc","after":"fe4f702bd0f879c9cf73cdfd5341c233a2fb470a","ref":"refs/heads/fix/rust_child_seq","pushedAt":"2024-04-12T11:23:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"test: adjust test input and test expectations","shortMessageHtmlLink":"test: adjust test input and test expectations"}},{"before":null,"after":"894e014c44c44657a6afff73b3fa2477a2fd31fc","ref":"refs/heads/fix/rust_child_seq","pushedAt":"2024-04-12T11:18:30.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"fix: modify child sequence as we gather mutations","shortMessageHtmlLink":"fix: modify child sequence as we gather mutations"}},{"before":"58d175895f35559749f1107e978d6df88fd63b9e","after":"f9d95f215ff0b71f54726b6c7d2d1098405dba04","ref":"refs/heads/rust","pushedAt":"2024-04-11T21:14:16.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"feat: port marginal reconstruction","shortMessageHtmlLink":"feat: port marginal reconstruction"}},{"before":"1f14dc1ed58587d7593e20812fa0aeb075046d6d","after":"58d175895f35559749f1107e978d6df88fd63b9e","ref":"refs/heads/rust","pushedAt":"2024-04-11T21:02:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"feat: port marginal reconstruction","shortMessageHtmlLink":"feat: port marginal reconstruction"}},{"before":"23a7a071628e7637d96e13433918a2c5fa387ac8","after":"1f14dc1ed58587d7593e20812fa0aeb075046d6d","ref":"refs/heads/rust","pushedAt":"2024-04-11T20:22:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ivan-aksamentov","name":"Ivan Aksamentov","path":"/ivan-aksamentov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9403403?s=80&v=4"},"commit":{"message":"feat: port outgroup_profiles()","shortMessageHtmlLink":"feat: port outgroup_profiles()"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEONtgIgA","startCursor":null,"endCursor":null}},"title":"Activity · neherlab/treetime"}