{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":493877605,"defaultBranch":"master","name":"mpox","ownerLogin":"nextstrain","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-05-19T01:19:17.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/22159334?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1727406292.0","currentOid":""},"activityList":{"items":[{"before":"ae63e43e1e36b504335cb7e2f7546eaee03e20d5","after":"937dfdd507d0d09686e644f8fdac38d3b5445428","ref":"refs/heads/james/inrb-mk2","pushedAt":"2024-09-29T20:19:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"[inrb] Update description markdown","shortMessageHtmlLink":"[inrb] Update description markdown"}},{"before":"6b4b47cb3e8af18d6ceadb31b84c991dde6ec0eb","after":"46c85b03ee8aebe387d3c72eb4328d80c9a899e8","ref":"refs/heads/james/inrb","pushedAt":"2024-09-27T03:13:26.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"INRB-specific configs\n\nParameters and description via email correspondence","shortMessageHtmlLink":"INRB-specific configs"}},{"before":null,"after":"ae63e43e1e36b504335cb7e2f7546eaee03e20d5","ref":"refs/heads/james/inrb-mk2","pushedAt":"2024-09-27T03:04:52.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"INRB-Metadata fixes\n\nThe aim is to allow DTA reconstruction for division and (perhaps)\nlocation.","shortMessageHtmlLink":"INRB-Metadata fixes"}},{"before":"65ca7416e5e6f1ca802d4e67d3273a6e4d14a0fa","after":"cd29467cb8bab174ce6a7c375edab86592702fd4","ref":"refs/heads/james/clade-i-tweaks","pushedAt":"2024-09-27T01:11:06.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"[clade-I] hardcode clade assignment\n\nThis approach is necessary because the mutations assigned to the top\nbranches in the tree are random. I'd consider this approach temporary\nand we should revisit it in the near-future.","shortMessageHtmlLink":"[clade-I] hardcode clade assignment"}},{"before":"02b4319edcd11da2781fd018bd48ceb196bde775","after":null,"ref":"refs/heads/james/geo-fixes","pushedAt":"2024-09-27T01:10:00.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"}},{"before":"2019e10418e9fc70692de4a395b23a4e8aafc90a","after":"b453693963b4eed7ab0937246b0bc2d18e49aa7c","ref":"refs/heads/master","pushedAt":"2024-09-27T01:09:59.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"Merge pull request #279 from nextstrain/james/geo-fixes\n\nUpdate geo-fixes","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2551788752\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/279\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/279/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/279\">#279</a> from nextstrain/james/geo-fixes"}},{"before":null,"after":"65ca7416e5e6f1ca802d4e67d3273a6e4d14a0fa","ref":"refs/heads/james/clade-i-tweaks","pushedAt":"2024-09-27T01:02:39.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"[clade-I] hardcode clade assignment\n\nThis approach is necessary because the mutations assigned to the top\nbranches in the tree are random. I'd consider this approach temporary\nand we should revisit it in the near-future.","shortMessageHtmlLink":"[clade-I] hardcode clade assignment"}},{"before":null,"after":"02b4319edcd11da2781fd018bd48ceb196bde775","ref":"refs/heads/james/geo-fixes","pushedAt":"2024-09-26T22:14:08.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"Update geo-fixes\n\nSee added comments in TSV","shortMessageHtmlLink":"Update geo-fixes"}},{"before":null,"after":"b77e8ccdb2eae63b2c1475f8f40d6d53ad18dec5","ref":"refs/heads/pre-commit-ci-update-config","pushedAt":"2024-09-23T22:23:56.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"pre-commit-ci[bot]","name":null,"path":"/apps/pre-commit-ci","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/68672?s=80&v=4"},"commit":{"message":"[pre-commit.ci] pre-commit autoupdate\n\nupdates:\n- [github.com/rhysd/actionlint: v1.7.1 → v1.7.2](https://github.com/rhysd/actionlint/compare/v1.7.1...v1.7.2)","shortMessageHtmlLink":"[pre-commit.ci] pre-commit autoupdate"}},{"before":"22e78f72407d612b7e49bccc3cd7f20d06dbac6e","after":"2019e10418e9fc70692de4a395b23a4e8aafc90a","ref":"refs/heads/master","pushedAt":"2024-08-27T07:03:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Fix changelog for mpox/all-clades","shortMessageHtmlLink":"Fix changelog for mpox/all-clades"}},{"before":"da3b295706ef045a3356146a87933659d552c7d6","after":null,"ref":"refs/heads/refactor","pushedAt":"2024-08-27T06:53:55.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"}},{"before":"61b6a6fb19aaf5b97986164765cd81bb3fe7b7a8","after":"22e78f72407d612b7e49bccc3cd7f20d06dbac6e","ref":"refs/heads/master","pushedAt":"2024-08-27T06:53:53.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Merge pull request #276 from nextstrain/refactor\n\nUpdate nextclade workflow","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2488453235\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/276\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/276/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/276\">#276</a> from nextstrain/refactor"}},{"before":"92f12e4de53210b000fd7eba0fe85aeb5825a8f6","after":"da3b295706ef045a3356146a87933659d552c7d6","ref":"refs/heads/refactor","pushedAt":"2024-08-27T06:52:57.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Update nextclade workflow","shortMessageHtmlLink":"Update nextclade workflow"}},{"before":null,"after":"92f12e4de53210b000fd7eba0fe85aeb5825a8f6","ref":"refs/heads/refactor","pushedAt":"2024-08-27T06:52:15.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Update nextclade workflow","shortMessageHtmlLink":"Update nextclade workflow"}},{"before":"7c049b79fdd01f569410292fede8e4a2f405e98a","after":null,"ref":"refs/heads/pre-commit-ci-update-config","pushedAt":"2024-08-27T06:07:40.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"}},{"before":"c948d4fba947d260194cbb261537eec5707f951b","after":"61b6a6fb19aaf5b97986164765cd81bb3fe7b7a8","ref":"refs/heads/master","pushedAt":"2024-08-27T06:07:39.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Merge pull request #253 from nextstrain/pre-commit-ci-update-config\n\n[pre-commit.ci] pre-commit autoupdate","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2293900283\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/253\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/253/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/253\">#253</a> from nextstrain/pre-commit-ci-update-config"}},{"before":"df0308937aa60337bdfa58aa94fe2d84a9db35c9","after":null,"ref":"refs/heads/clade-def-and-coloring","pushedAt":"2024-08-27T06:06:10.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"}},{"before":"cf9d07221eaa7e02890f4cf28346c1b94e058a9f","after":"c948d4fba947d260194cbb261537eec5707f951b","ref":"refs/heads/master","pushedAt":"2024-08-27T06:06:08.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Merge pull request #274 from nextstrain/clade-def-and-coloring\n\nUpdate clade definition and coloring","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2483916539\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/274\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/274/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/274\">#274</a> from nextstrain/clade-def-and-coloring"}},{"before":null,"after":"4a268babe797bc4361444fc7cf2ae434129d1da2","ref":"refs/heads/james/node-name-accession","pushedAt":"2024-08-26T03:55:30.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"Use accession for node name but display strain\n\nThis is a companion commit to changes in Auspice <https://github.com/nextstrain/auspice/pull/1668>\nwhich allow any node-attr to be used as the tip label and which displays\nthis tip label in the node hover/click boxes as well as alongside nodes\n(at suitable zoom levels). This allows us to drop the `set_final_strain_name`\nscript and ensures all node names are unique which improves the behaviour\nof Auspice\n\nThis commit only changes the Nextstrain datasets, not the Nextclade ones","shortMessageHtmlLink":"Use accession for node name but display strain"}},{"before":null,"after":"df0308937aa60337bdfa58aa94fe2d84a9db35c9","ref":"refs/heads/clade-def-and-coloring","pushedAt":"2024-08-23T21:18:43.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"trvrb","name":"Trevor Bedford","path":"/trvrb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1176109?s=80&v=4"},"commit":{"message":"Update clade definition and coloring\n\nThis commit:\n\n1. Very slightly changes clade definition for \"clade II\". This results in no change to the resulting clade assignments.\n\nPreviously clade II definitions included nucleotide positions 35253 and 150970. However, neither of these positions show variation:\n- nextstrain.org/mpox/all-clades?c=gt-nuc_35253\n- nextstrain.org/mpox/all-clades?c=gt-nuc_150970\n\nI updated these sites to 20605 and 174146 which show variation between clades I and II.\n\n2. The color ordering lacked entries for clade Ia and clade Ib. This resulted in gray colors for these two clades at nextstrain.org/mpox/all-clades.","shortMessageHtmlLink":"Update clade definition and coloring"}},{"before":"2ce0d9284ccc8cf9b06e8094c7fa28c8f9d85771","after":"cf9d07221eaa7e02890f4cf28346c1b94e058a9f","ref":"refs/heads/master","pushedAt":"2024-08-23T21:11:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvrb","name":"Trevor Bedford","path":"/trvrb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1176109?s=80&v=4"},"commit":{"message":"Update outliers","shortMessageHtmlLink":"Update outliers"}},{"before":"59b3edf5f90fcf59a08f70459674380bdb2e352e","after":null,"ref":"refs/heads/phylo-update-clades","pushedAt":"2024-08-15T21:09:39.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"}},{"before":"9d3b8ea9f5b4916c3459a6796fda4fc823b54951","after":"2ce0d9284ccc8cf9b06e8094c7fa28c8f9d85771","ref":"refs/heads/master","pushedAt":"2024-08-15T21:09:38.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Merge pull request #270 from nextstrain/phylo-update-clades\n\nPhylo update clades","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2468928997\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/270\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/270/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/270\">#270</a> from nextstrain/phylo-update-clades"}},{"before":null,"after":"59b3edf5f90fcf59a08f70459674380bdb2e352e","ref":"refs/heads/phylo-update-clades","pushedAt":"2024-08-15T20:48:08.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"joverlee521","name":"Jover Lee","path":"/joverlee521","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40774762?s=80&v=4"},"commit":{"message":"phylogenetic: Update clades.tsv\n\nResolving additional differences I noticed between this clades.tsv\nand the nextclade clades.tsv\n\n<https://github.com/nextstrain/mpox/blob/9d3b8ea9f5b4916c3459a6796fda4fc823b54951/nextclade/resources/all-clades/clades.tsv>","shortMessageHtmlLink":"phylogenetic: Update clades.tsv"}},{"before":"5e52962a782045cb31a958da0138b06e8e362c6d","after":null,"ref":"refs/heads/refactor","pushedAt":"2024-08-14T20:06:05.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"}},{"before":"077119624db611048d8f3ce716120a9ec883e2c3","after":"9d3b8ea9f5b4916c3459a6796fda4fc823b54951","ref":"refs/heads/master","pushedAt":"2024-08-14T20:06:03.000Z","pushType":"pr_merge","commitsCount":9,"pusher":{"login":"rneher","name":"Richard Neher","path":"/rneher","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8379168?s=80&v=4"},"commit":{"message":"Merge pull request #268 from nextstrain/refactor\n\nAdding clade I Nextclade build and other small refactorings","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2466585279\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/268\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/268/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/268\">#268</a> from nextstrain/refactor"}},{"before":"bc76667e237858eab4e7ce63198a0ab2e817d154","after":"5e52962a782045cb31a958da0138b06e8e362c6d","ref":"refs/heads/refactor","pushedAt":"2024-08-14T18:49:37.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Clade I example sequences","shortMessageHtmlLink":"Clade I example sequences"}},{"before":"cd6bec0dd0782a25aa0b3c02a2512133271004ec","after":null,"ref":"refs/heads/update-description","pushedAt":"2024-08-13T17:06:49.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"joverlee521","name":"Jover Lee","path":"/joverlee521","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40774762?s=80&v=4"}},{"before":"1889dffba6af2b5aeb8b3d38aa76064095aa4030","after":"077119624db611048d8f3ce716120a9ec883e2c3","ref":"refs/heads/master","pushedAt":"2024-08-13T17:06:48.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"joverlee521","name":"Jover Lee","path":"/joverlee521","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40774762?s=80&v=4"},"commit":{"message":"Merge pull request #267 from nextstrain/update-description\n\nUpdate description","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2458402402\" data-permission-text=\"Title is private\" data-url=\"https://github.com/nextstrain/mpox/issues/267\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/nextstrain/mpox/pull/267/hovercard\" href=\"https://github.com/nextstrain/mpox/pull/267\">#267</a> from nextstrain/update-description"}},{"before":null,"after":"cd6bec0dd0782a25aa0b3c02a2512133271004ec","ref":"refs/heads/update-description","pushedAt":"2024-08-09T17:51:26.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"joverlee521","name":"Jover Lee","path":"/joverlee521","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40774762?s=80&v=4"},"commit":{"message":"description: Add link to clade I build","shortMessageHtmlLink":"description: Add link to clade I build"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yOVQyMDoxOTo0NS4wMDAwMDBazwAAAATEC_HY","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOC0wOVQxNzo1MToyNi4wMDAwMDBazwAAAASWg3v0"}},"title":"Activity · nextstrain/mpox"}