{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":259668243,"defaultBranch":"master","name":"PhyloFisher","ownerLogin":"TheBrownLab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-04-28T14:56:44.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/64451965?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1716936764.0","currentOid":""},"activityList":{"items":[{"before":"d64e291ee1adf16642c5ee1dc0ba40004dd72004","after":"13ac7c893a0fd570adff42becccc77983f430952","ref":"refs/heads/master","pushedAt":"2024-05-29T19:20:58.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Fix the bug in issue#120 \"NameError: name 'metadata' is not defined\" (#121)\n\n* Update forest_local.py\r\n\r\nRemove multiprocessing to fix the bug in issue #120 \"metadata not defined in forest_local.py\"(and import PyQt5 for ete3, I'm not sure if it's necessary.).\r\n\r\n* Update forest_local.py\r\n\r\nOnly fix the bug in issue #120.\r\n\r\n* Update matrix_constructor.py\r\n\r\nTo fix the snakemake bug \"MissingRuleException:\r\nNo rule to produce snakemake (if you use input functions make sure that they don't raise unexpected exceptions).\" \r\nIt's caused by \"--of phylip\" because in original code, one of output file \"matrix.fas\" in python didn't match the name \"f'{out_dir}/matrix.{out_dict[out_format.lower()]}'\"(if use default --of fasta, they are thesame) in snakemake file.\r\n\r\n---------\r\n\r\nCo-authored-by: Robert E. Jones <56359883+robert-ervin-jones@users.noreply.github.com>","shortMessageHtmlLink":"Fix the bug in issue#120 \"NameError: name 'metadata' is not defined\" (#…"}},{"before":"662bd8028fa992e138b70e7d71b9c59c2025abef","after":null,"ref":"refs/heads/adds-leaf-rename-utility","pushedAt":"2024-05-28T22:52:44.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"fd6bc4da49461caa0bb55040e7eeddeca334a13f","after":"d64e291ee1adf16642c5ee1dc0ba40004dd72004","ref":"refs/heads/master","pushedAt":"2024-05-28T22:52:41.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"add leaf rename utility (#117)","shortMessageHtmlLink":"add leaf rename utility (#117)"}},{"before":"02b684b2675db0fdc2ecc4648156c42f9d3e0e8c","after":"662bd8028fa992e138b70e7d71b9c59c2025abef","ref":"refs/heads/adds-leaf-rename-utility","pushedAt":"2024-05-28T22:50:29.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Merge branch 'master' into adds-leaf-rename-utility","shortMessageHtmlLink":"Merge branch 'master' into adds-leaf-rename-utility"}},{"before":"953be474962876657906f324d41f1f29ec6bc414","after":null,"ref":"refs/heads/integrates-nucl-matrix-contsructor","pushedAt":"2024-05-28T22:50:18.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"fdfc09d4d1af80450e9b437ed3c71f939893d59d","after":"fd6bc4da49461caa0bb55040e7eeddeca334a13f","ref":"refs/heads/master","pushedAt":"2024-05-28T22:50:12.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Integrates nucl matrix contsructor (#118)\n\n* renames cds header and checks if provided cds is actually nucleotides\r\n\r\n* accepts cds that are tar.gz\r\n\r\n* adds nucl_matrix to setup.py","shortMessageHtmlLink":"Integrates nucl matrix contsructor (#118)"}},{"before":"bbe809a4c73fe6ca9f4ba255dad414c6a227594f","after":"953be474962876657906f324d41f1f29ec6bc414","ref":"refs/heads/integrates-nucl-matrix-contsructor","pushedAt":"2024-02-19T19:04:54.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Merge branch 'master' into integrates-nucl-matrix-contsructor","shortMessageHtmlLink":"Merge branch 'master' into integrates-nucl-matrix-contsructor"}},{"before":null,"after":"bbe809a4c73fe6ca9f4ba255dad414c6a227594f","ref":"refs/heads/integrates-nucl-matrix-contsructor","pushedAt":"2024-02-19T19:00:50.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"adds nucl_matrix to setup.py","shortMessageHtmlLink":"adds nucl_matrix to setup.py"}},{"before":"7cd872f064e07ef9f5f5edaa9b46d251a6d589e4","after":"02b684b2675db0fdc2ecc4648156c42f9d3e0e8c","ref":"refs/heads/adds-leaf-rename-utility","pushedAt":"2024-02-19T18:55:46.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Merge branch 'master' into adds-leaf-rename-utility","shortMessageHtmlLink":"Merge branch 'master' into adds-leaf-rename-utility"}},{"before":null,"after":"7cd872f064e07ef9f5f5edaa9b46d251a6d589e4","ref":"refs/heads/adds-leaf-rename-utility","pushedAt":"2024-02-19T18:52:38.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"add leaf rename utility","shortMessageHtmlLink":"add leaf rename utility"}},{"before":"8782d6af5cf52106cbd31eb4306e090252afd081","after":"fdfc09d4d1af80450e9b437ed3c71f939893d59d","ref":"refs/heads/master","pushedAt":"2024-02-19T18:51:16.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"fix typo matrix_constructor.smk (#114)\n\nCo-authored-by: Robert E. Jones <56359883+robert-ervin-jones@users.noreply.github.com>","shortMessageHtmlLink":"fix typo matrix_constructor.smk (#114)"}},{"before":"29b0dbf97760eb6aa7ec7a40a28405e4c0f85588","after":null,"ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-19T18:48:00.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"9b98bbbef2975a730092138f258a947e60e3a936","after":"8782d6af5cf52106cbd31eb4306e090252afd081","ref":"refs/heads/master","pushedAt":"2024-02-19T18:47:57.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Add .circleci/config.yml (#115)\n\n* Add .circleci/config.yml\r\n\r\n* relax python requirement\r\n\r\n* removes test job\r\n\r\n* removes test job","shortMessageHtmlLink":"Add .circleci/config.yml (#115)"}},{"before":"c9fcfe957754f49e2ac2e841c8dc96f7702aee67","after":"29b0dbf97760eb6aa7ec7a40a28405e4c0f85588","ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-19T18:43:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"removes test job","shortMessageHtmlLink":"removes test job"}},{"before":"31bcab631660d414936371336ad51ec40ccbb5de","after":"c9fcfe957754f49e2ac2e841c8dc96f7702aee67","ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-19T18:39:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"removes test job","shortMessageHtmlLink":"removes test job"}},{"before":"8e417380074cacb6903f8f230e5a22fc4ba338b7","after":"31bcab631660d414936371336ad51ec40ccbb5de","ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-11T18:29:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"relax python requirement","shortMessageHtmlLink":"relax python requirement"}},{"before":"9b98bbbef2975a730092138f258a947e60e3a936","after":"8e417380074cacb6903f8f230e5a22fc4ba338b7","ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-11T18:24:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Add .circleci/config.yml","shortMessageHtmlLink":"Add .circleci/config.yml"}},{"before":null,"after":"9b98bbbef2975a730092138f258a947e60e3a936","ref":"refs/heads/circleci-project-setup","pushedAt":"2024-02-11T18:24:48.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"updates raxml tree path (#104)","shortMessageHtmlLink":"updates raxml tree path (#104)"}},{"before":"6a36947f6bbbd34f62d8ded1ad7ab852b4b78520","after":null,"ref":"refs/heads/102-no-bootstrap-values","pushedAt":"2023-10-26T15:24:59.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"711baa7b34131cf7df63e373efe4aeab414db3cf","after":"9b98bbbef2975a730092138f258a947e60e3a936","ref":"refs/heads/master","pushedAt":"2023-10-26T15:24:55.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"updates raxml tree path (#104)","shortMessageHtmlLink":"updates raxml tree path (#104)"}},{"before":"711baa7b34131cf7df63e373efe4aeab414db3cf","after":"6a36947f6bbbd34f62d8ded1ad7ab852b4b78520","ref":"refs/heads/102-no-bootstrap-values","pushedAt":"2023-10-26T15:20:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"updates raxml tree path","shortMessageHtmlLink":"updates raxml tree path"}},{"before":null,"after":"711baa7b34131cf7df63e373efe4aeab414db3cf","ref":"refs/heads/102-no-bootstrap-values","pushedAt":"2023-10-26T15:14:17.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Updates raxml ng (#103)\n\n* updates pipeline to copy support file\r\n\r\n* adds backup when rename option is used\r\n\r\n* bumps version","shortMessageHtmlLink":"Updates raxml ng (#103)"}},{"before":"be1824b23df951b6fa6c1ffe54ed4ff0cd009021","after":null,"ref":"refs/heads/updates-raxml-ng","pushedAt":"2023-10-09T21:03:53.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"4dd0079d4166de9e73a79b2a2c97723a2ab720a3","after":"711baa7b34131cf7df63e373efe4aeab414db3cf","ref":"refs/heads/master","pushedAt":"2023-10-09T21:03:48.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Updates raxml ng (#103)\n\n* updates pipeline to copy support file\r\n\r\n* adds backup when rename option is used\r\n\r\n* bumps version","shortMessageHtmlLink":"Updates raxml ng (#103)"}},{"before":null,"after":"be1824b23df951b6fa6c1ffe54ed4ff0cd009021","ref":"refs/heads/updates-raxml-ng","pushedAt":"2023-10-09T17:53:38.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"bumps version","shortMessageHtmlLink":"bumps version"}},{"before":"a90c28c4563561ec638f218535722baf706d9386","after":null,"ref":"refs/heads/adds-sht-include-to-informant","pushedAt":"2023-09-12T16:27:17.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"}},{"before":"52ebad88cf59ad346af8877595f8aba429a2c21a","after":"4dd0079d4166de9e73a79b2a2c97723a2ab720a3","ref":"refs/heads/master","pushedAt":"2023-09-12T16:27:13.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"adds sht_include option to informant (#97)\n\n* adds sht_include option to informant\r\n\r\n* bumps version\r\n\r\n* updates option name","shortMessageHtmlLink":"adds sht_include option to informant (#97)"}},{"before":"b4b4585af48d723598b33e165fa6d6b7e04d5fb6","after":"a90c28c4563561ec638f218535722baf706d9386","ref":"refs/heads/adds-sht-include-to-informant","pushedAt":"2023-09-12T16:19:14.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"Merge branch 'master' into adds-sht-include-to-informant","shortMessageHtmlLink":"Merge branch 'master' into adds-sht-include-to-informant"}},{"before":"1677539d8930e324fa3001a372c053baa9bfbce4","after":"b4b4585af48d723598b33e165fa6d6b7e04d5fb6","ref":"refs/heads/adds-sht-include-to-informant","pushedAt":"2023-09-12T16:04:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"updates option name","shortMessageHtmlLink":"updates option name"}},{"before":"2f1f1bbc126dc65ed4087276558c6feca85e6758","after":"1677539d8930e324fa3001a372c053baa9bfbce4","ref":"refs/heads/adds-sht-include-to-informant","pushedAt":"2023-09-12T15:58:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"robert-ervin-jones","name":"Robert E. Jones","path":"/robert-ervin-jones","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56359883?s=80&v=4"},"commit":{"message":"bumps version","shortMessageHtmlLink":"bumps version"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEV08yZAA","startCursor":null,"endCursor":null}},"title":"Activity · TheBrownLab/PhyloFisher"}