{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":514345480,"defaultBranch":"main","name":"cov-voc","ownerLogin":"jt-lanl","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-07-15T17:05:06.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/75394476?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1709439940.0","currentOid":""},"activityList":{"items":[{"before":"35dcd5732909be35e55a16c80c3209aae5b2e140","after":"165de5019db0884c2547c439123221cd6527c616","ref":"refs/heads/main","pushedAt":"2024-06-24T01:00:16.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"New lineage table version: v33","shortMessageHtmlLink":"New lineage table version: v33"}},{"before":"65651e2c37748e3b6f6fdbca149593662f74d698","after":"35dcd5732909be35e55a16c80c3209aae5b2e140","ref":"refs/heads/main","pushedAt":"2024-05-24T20:33:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"disable args.baseline if protein is not Spike","shortMessageHtmlLink":"disable args.baseline if protein is not Spike"}},{"before":"f8c9bba8c1cddd5979f9e25ae77e9838e640ca61","after":"65651e2c37748e3b6f6fdbca149593662f74d698","ref":"refs/heads/main","pushedAt":"2024-05-15T20:52:41.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"re-implement date filtering to avoid deprecated covid.date_range_from_args()","shortMessageHtmlLink":"re-implement date filtering to avoid deprecated covid.date_range_from…"}},{"before":"63534f9af6341c4465edee0518793eb086c296a1","after":"f8c9bba8c1cddd5979f9e25ae77e9838e640ca61","ref":"refs/heads/main","pushedAt":"2024-05-14T16:53:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"new error if trying to read stdin with --days invoked","shortMessageHtmlLink":"new error if trying to read stdin with --days invoked"}},{"before":"80ff0fa538244e4b60e8dede15f4e016163c6c43","after":"63534f9af6341c4465edee0518793eb086c296a1","ref":"refs/heads/main","pushedAt":"2024-05-14T16:41:52.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"use covid.py code to read seqfile twice of --days is set","shortMessageHtmlLink":"use covid.py code to read seqfile twice of --days is set"}},{"before":"f9c445b1677447138c7a17427bce1346c332a1a7","after":"80ff0fa538244e4b60e8dede15f4e016163c6c43","ref":"refs/heads/main","pushedAt":"2024-05-09T20:20:28.000Z","pushType":"push","commitsCount":40,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"mostly just reformatted","shortMessageHtmlLink":"mostly just reformatted"}},{"before":"b047d77855692bfdd617129ffe6be3d78f8e0587","after":"f9c445b1677447138c7a17427bce1346c332a1a7","ref":"refs/heads/main","pushedAt":"2024-03-18T03:21:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"cleaned up logic in checktweaks function","shortMessageHtmlLink":"cleaned up logic in checktweaks function"}},{"before":"008913e32f5c04be6ccf00285558e3c9fa220da8","after":"b047d77855692bfdd617129ffe6be3d78f8e0587","ref":"refs/heads/main","pushedAt":"2024-03-17T22:38:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"added more elaborate output for --checktweaks option","shortMessageHtmlLink":"added more elaborate output for --checktweaks option"}},{"before":"04656b24e4de71e7665e1dbeaea62af8ff2074b8","after":"008913e32f5c04be6ccf00285558e3c9fa220da8","ref":"refs/heads/main","pushedAt":"2024-03-17T03:26:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"small adjustment to order of lineages in v31","shortMessageHtmlLink":"small adjustment to order of lineages in v31"}},{"before":"b86c6a2319b18fc9af576d3bbe9ffe7537bc6dcf","after":"04656b24e4de71e7665e1dbeaea62af8ff2074b8","ref":"refs/heads/main","pushedAt":"2024-03-17T02:35:30.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"updated to v31","shortMessageHtmlLink":"updated to v31"}},{"before":"45f8a0a42910e38abb52bdb863e6ee477c6d1c69","after":"b86c6a2319b18fc9af576d3bbe9ffe7537bc6dcf","ref":"refs/heads/main","pushedAt":"2024-03-16T18:27:00.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"work around edge case that cases mutpair_to_mstringpair function to fail -- by avoiding that function","shortMessageHtmlLink":"work around edge case that cases mutpair_to_mstringpair function to f…"}},{"before":"4ba210edd48248fc6e4c9acfce37a52d1f0f514b","after":"45f8a0a42910e38abb52bdb863e6ee477c6d1c69","ref":"refs/heads/main","pushedAt":"2024-03-12T18:14:43.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"adjust both leading /and/ trailing characters in the tweak strings to trim common characters","shortMessageHtmlLink":"adjust both leading /and/ trailing characters in the tweak strings to…"}},{"before":"7d2a2c97400d3783bc968e5f02991da1821127fb","after":"4ba210edd48248fc6e4c9acfce37a52d1f0f514b","ref":"refs/heads/main","pushedAt":"2024-03-12T00:52:51.000Z","pushType":"push","commitsCount":18,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"eanble matches to pattrns that lead with an insertion -- eg, [+18I,T19T,T20T,R21-]","shortMessageHtmlLink":"eanble matches to pattrns that lead with an insertion -- eg, [+18I,T1…"}},{"before":"ecbade7445ae0a1045edc6cf6108d74bd4fa132f","after":"7d2a2c97400d3783bc968e5f02991da1821127fb","ref":"refs/heads/main","pushedAt":"2024-03-07T17:41:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"works with mulitple reference seqeunces","shortMessageHtmlLink":"works with mulitple reference seqeunces"}},{"before":"f31de4f15147ad1eefaa1f927644485ac05f6019","after":"ecbade7445ae0a1045edc6cf6108d74bd4fa132f","ref":"refs/heads/main","pushedAt":"2024-03-06T05:16:29.000Z","pushType":"push","commitsCount":18,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"minor; warning messages are more informative","shortMessageHtmlLink":"minor; warning messages are more informative"}},{"before":"3226fcf36fa4e4869ba705997f2d373b9fc78e47","after":"f31de4f15147ad1eefaa1f927644485ac05f6019","ref":"refs/heads/main","pushedAt":"2024-03-04T17:24:30.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"module for IndexTweak class, and general utilities for alignment tweaks","shortMessageHtmlLink":"module for IndexTweak class, and general utilities for alignment tweaks"}},{"before":"abfc04400506cccfa30d23915e66172c2e5a5ebc","after":"3226fcf36fa4e4869ba705997f2d373b9fc78e47","ref":"refs/heads/main","pushedAt":"2024-03-03T04:24:17.000Z","pushType":"push","commitsCount":18,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"mostly minor, some updates to arg processing","shortMessageHtmlLink":"mostly minor, some updates to arg processing"}},{"before":"e96affa88e0fe65ca64514493f2f08f7ffec750b","after":"abfc04400506cccfa30d23915e66172c2e5a5ebc","ref":"refs/heads/main","pushedAt":"2024-02-12T20:25:04.000Z","pushType":"push","commitsCount":11,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"added --viz and --output options","shortMessageHtmlLink":"added --viz and --output options"}},{"before":"681e7c896cb335d6595239dc423880f2fd475771","after":"e96affa88e0fe65ca64514493f2f08f7ffec750b","ref":"refs/heads/main","pushedAt":"2024-02-10T00:06:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"use reference name that is not specific to Spike","shortMessageHtmlLink":"use reference name that is not specific to Spike"}},{"before":"29369afd81652f5299d037eabf3be7b0ee5703e1","after":"681e7c896cb335d6595239dc423880f2fd475771","ref":"refs/heads/main","pushedAt":"2024-02-09T20:01:10.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"added caveat as a comment","shortMessageHtmlLink":"added caveat as a comment"}},{"before":"13fcc280f4a3d99250548e6db58d7acb13457e0a","after":"29369afd81652f5299d037eabf3be7b0ee5703e1","ref":"refs/heads/main","pushedAt":"2024-02-08T07:38:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"altered handling of DEFAULTNAMESFILE; now complain about its absense /only/ if no input file is specified","shortMessageHtmlLink":"altered handling of DEFAULTNAMESFILE; now complain about its absense …"}},{"before":"09b36e3f8310768685c9cf2971e113cec5d7dea2","after":"13fcc280f4a3d99250548e6db58d7acb13457e0a","ref":"refs/heads/main","pushedAt":"2024-02-07T19:30:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"Parallel Python -m; replace \"pm\" with \"ppm\" for parallel processing of /certain/ cov-voc routines: fixfasta, matchfasta, tweakfasta among them","shortMessageHtmlLink":"Parallel Python -m; replace \"pm\" with \"ppm\" for parallel processing o…"}},{"before":"173c0387fee9f464047ba46e85bff5d2dc8ac31f","after":"09b36e3f8310768685c9cf2971e113cec5d7dea2","ref":"refs/heads/main","pushedAt":"2024-02-07T17:59:59.000Z","pushType":"push","commitsCount":53,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"minor adjustment to verbosity levels","shortMessageHtmlLink":"minor adjustment to verbosity levels"}},{"before":"1e4d71dfa59abf4dc794e3f15ed6ef3bd08e5ad2","after":"173c0387fee9f464047ba46e85bff5d2dc8ac31f","ref":"refs/heads/main","pushedAt":"2024-01-31T04:35:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"baseline not case sensive; more common code (such as args) now in commonforms.py","shortMessageHtmlLink":"baseline not case sensive; more common code (such as args) now in com…"}},{"before":"2698daedc545cd644b9f02f2e2dabcbf866677d6","after":"1e4d71dfa59abf4dc794e3f15ed6ef3bd08e5ad2","ref":"refs/heads/main","pushedAt":"2024-01-30T15:29:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"fixed interaction of --baseline and --lineagebaseline","shortMessageHtmlLink":"fixed interaction of --baseline and --lineagebaseline"}},{"before":"ca64322248761c6fdd733f927927939f2b0d2970","after":"2698daedc545cd644b9f02f2e2dabcbf866677d6","ref":"refs/heads/main","pushedAt":"2024-01-29T22:04:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"revert to older: @cache->@lru_cache, fstring {expr=}->expr={expr}","shortMessageHtmlLink":"revert to older: @cache->@lru_cache, fstring {expr=}->expr={expr}"}},{"before":"005f18db9be005fedc990aadaf400cfddc380d7c","after":"ca64322248761c6fdd733f927927939f2b0d2970","ref":"refs/heads/main","pushedAt":"2024-01-29T20:41:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"replace f-strings {expr=} with older-style expr={expr}","shortMessageHtmlLink":"replace f-strings {expr=} with older-style expr={expr}"}},{"before":"8e0aeab64786b35d77d3e22ab122c4b8373d7103","after":"005f18db9be005fedc990aadaf400cfddc380d7c","ref":"refs/heads/main","pushedAt":"2024-01-29T04:10:13.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"cleaned up code, smarter mstring pairs","shortMessageHtmlLink":"cleaned up code, smarter mstring pairs"}},{"before":"4796a1b70dee3955735f9b9241c98f4a9d20d7de","after":"8e0aeab64786b35d77d3e22ab122c4b8373d7103","ref":"refs/heads/main","pushedAt":"2024-01-28T19:44:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"added five new tweaks","shortMessageHtmlLink":"added five new tweaks"}},{"before":"526085439199dc076be28e9ecdb2c36d2bbbcbf5","after":"4796a1b70dee3955735f9b9241c98f4a9d20d7de","ref":"refs/heads/main","pushedAt":"2024-01-27T21:45:09.000Z","pushType":"push","commitsCount":20,"pusher":{"login":"jt-lanl","name":"James Theiler","path":"/jt-lanl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/75394476?s=80&v=4"},"commit":{"message":"added --count option to just count matches","shortMessageHtmlLink":"added --count option to just count matches"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEbQHVlgA","startCursor":null,"endCursor":null}},"title":"Activity · jt-lanl/cov-voc"}