{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":313429990,"defaultBranch":"main","name":"Snekmer","ownerLogin":"PNNL-CompBio","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-11-16T21:20:56.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/38365343?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1713906832.0","currentOid":""},"activityList":{"items":[{"before":"22dd1c5cd962d2a976d76f7dd5f10b4d46e21268","after":"163239c75f082757b8c67d95e3f15e5240c183b9","ref":"refs/heads/background","pushedAt":"2024-05-10T18:31:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"[skip ci] docs: add error catching for missing bg files in c/bg mode","shortMessageHtmlLink":"[skip ci] docs: add error catching for missing bg files in c/bg mode"}},{"before":"143a6484666fe35cc42e1c97f47743aa00b21cfb","after":"742d5cb4f3f45cd62f4f3f6987aac4eb2564375f","ref":"refs/heads/Environment_fix","pushedAt":"2024-05-08T21:02:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"fix: pin hdbscan version. install snekmer directly from pip\n\nchangelog:\n- Require hdbscan >= 0.8.29 to resolve installation errors (see: https://github.com/scikit-learn-contrib/hdbscan/issues/565)\n- Directly use available pip installable version of snekmer instead of git+github functionality","shortMessageHtmlLink":"fix: pin hdbscan version. install snekmer directly from pip"}},{"before":"c40e09f597500a4c6384545fd59886ea771cdd27","after":"22dd1c5cd962d2a976d76f7dd5f10b4d46e21268","ref":"refs/heads/background","pushedAt":"2024-05-08T20:58:45.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"build: force new versions of hdbscan to bypass install errors","shortMessageHtmlLink":"build: force new versions of hdbscan to bypass install errors"}},{"before":"679af3d0eeac0bd705fca048840c9f0fe339f7c0","after":"c40e09f597500a4c6384545fd59886ea771cdd27","ref":"refs/heads/background","pushedAt":"2024-05-07T17:57:09.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"refactor: remove commented (outdated) code","shortMessageHtmlLink":"refactor: remove commented (outdated) code"}},{"before":"155e36cdd18820550ef9d96831ef616de94b522c","after":"143a6484666fe35cc42e1c97f47743aa00b21cfb","ref":"refs/heads/Environment_fix","pushedAt":"2024-04-23T21:33:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"pin numpy to 1.22.3 when using the Blazing Signature Filter and on Windows","shortMessageHtmlLink":"pin numpy to 1.22.3 when using the Blazing Signature Filter and on Wi…"}},{"before":null,"after":"155e36cdd18820550ef9d96831ef616de94b522c","ref":"refs/heads/Environment_fix","pushedAt":"2024-04-23T21:13:52.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"skip-ci,docs: Update README.md\n\nAdd learn/apply details to README","shortMessageHtmlLink":"skip-ci,docs: Update README.md"}},{"before":"710d2ba0db668002f1253993cd20c91407a4ffc9","after":"679af3d0eeac0bd705fca048840c9f0fe339f7c0","ref":"refs/heads/background","pushedAt":"2024-04-16T21:26:59.000Z","pushType":"push","commitsCount":16,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"chore: update branch with changes to main","shortMessageHtmlLink":"chore: update branch with changes to main"}},{"before":"ba6df730d3d80175c88b61255be8c382fe356e66","after":"710d2ba0db668002f1253993cd20c91407a4ffc9","ref":"refs/heads/background","pushedAt":"2024-04-16T21:06:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"refactor: move kmerize to scripts. replace lists with numpy arrays","shortMessageHtmlLink":"refactor: move kmerize to scripts. replace lists with numpy arrays"}},{"before":"cdb04f78edc15d408f1c66a0b4efef3c721948cc","after":"4d864394d773a6d911a4d0b6834e5d8670dbf126","ref":"refs/heads/functionmotifs","pushedAt":"2024-03-26T19:36:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"move Motif tutorial into separate directory with more informative config parameters","shortMessageHtmlLink":"move Motif tutorial into separate directory with more informative con…"}},{"before":"3d223f4f3fb4f84319d411e480d9730669a8fafc","after":"a7f7c1c642ee7a2dd38bb01331cb96a2d95dc49c","ref":"refs/heads/package","pushedAt":"2024-03-19T22:29:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"build: require python 3.9+","shortMessageHtmlLink":"build: require python 3.9+"}},{"before":"4ff1b0a1ab5bc3cf70d370fbf9e697db0c17959c","after":"cdb04f78edc15d408f1c66a0b4efef3c721948cc","ref":"refs/heads/functionmotifs","pushedAt":"2024-03-15T19:37:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Remove redundant code from motif result script","shortMessageHtmlLink":"Remove redundant code from motif result script"}},{"before":"56f660776c0e6f526c6313ffadd6bae45bf69a2f","after":"4ff1b0a1ab5bc3cf70d370fbf9e697db0c17959c","ref":"refs/heads/functionmotifs","pushedAt":"2024-03-15T17:59:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Fix formatting","shortMessageHtmlLink":"Fix formatting"}},{"before":"d9e3a6bfeab935913b041add08bce555689fef47","after":"3d223f4f3fb4f84319d411e480d9730669a8fafc","ref":"refs/heads/package","pushedAt":"2024-03-13T23:51:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"build: update pip install links for snekmer to pypi","shortMessageHtmlLink":"build: update pip install links for snekmer to pypi"}},{"before":null,"after":"d9e3a6bfeab935913b041add08bce555689fef47","ref":"refs/heads/package","pushedAt":"2024-03-13T23:24:01.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"build: create pyproject.toml for pypi install (fixes #119)\n\nchangelog:\n- created pyproject.toml for snekmer installation\n- remove setup.py (no longer needed / deprecated)\n- `pip install snekmer` should now work`","shortMessageHtmlLink":"build: create pyproject.toml for pypi install (fixes #119)"}},{"before":"20023fdd2f2b3e4bc46664b4d0607ea1dfc7abf2","after":"ba6df730d3d80175c88b61255be8c382fe356e66","ref":"refs/heads/background","pushedAt":"2024-03-13T19:38:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"refactor: remove extraneous variables and verbose code","shortMessageHtmlLink":"refactor: remove extraneous variables and verbose code"}},{"before":"6924e9e69f2de0e765ef54c0cd0a44b2273bd1cf","after":"56f660776c0e6f526c6313ffadd6bae45bf69a2f","ref":"refs/heads/functionmotifs","pushedAt":"2024-03-05T21:58:32.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"docs: clean up files and update/create symlinks\n\nchangelog:\n- removed ~HEAD notebook file\n- moved learn/apply and motif tutorial notebooks to docs folders to add them into sphinx documentation\n- created symlinks for the above notebooks so that notebooks are still accessible from the resources directory","shortMessageHtmlLink":"docs: clean up files and update/create symlinks"}},{"before":"aa1c11d5b20eb3515d4db582c208cde99b93d990","after":"6924e9e69f2de0e765ef54c0cd0a44b2273bd1cf","ref":"refs/heads/functionmotifs","pushedAt":"2024-02-21T19:18:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Add motif report output","shortMessageHtmlLink":"Add motif report output"}},{"before":"43a8ccf6c426cd3584f91b1b7cf1d0ea9f54f06c","after":"20023fdd2f2b3e4bc46664b4d0607ea1dfc7abf2","ref":"refs/heads/background","pushedAt":"2024-02-20T21:59:34.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"fix,refactor: resolve array shapes. streamline code\n\nchangelog:\n- fix: resolve error with array shapes due to matrix dimensions (transpose matrix required)\n- refactor: renamed variables to streamline code","shortMessageHtmlLink":"fix,refactor: resolve array shapes. streamline code"}},{"before":"9c47a7ab925583e7a4cd004f0d2209ade5c55c0b","after":"aa1c11d5b20eb3515d4db582c208cde99b93d990","ref":"refs/heads/functionmotifs","pushedAt":"2024-02-02T20:12:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Fix formatting","shortMessageHtmlLink":"Fix formatting"}},{"before":"22f0a02a146b36a99be6f8d433cd6d7492860c3d","after":"9c47a7ab925583e7a4cd004f0d2209ade5c55c0b","ref":"refs/heads/functionmotifs","pushedAt":"2024-02-02T19:55:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Update documentation for motif","shortMessageHtmlLink":"Update documentation for motif"}},{"before":"8db7a279a504030f75f3788ddb1e9ced3ff1eca4","after":"22f0a02a146b36a99be6f8d433cd6d7492860c3d","ref":"refs/heads/functionmotifs","pushedAt":"2024-02-01T23:34:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Update docs to include motif","shortMessageHtmlLink":"Update docs to include motif"}},{"before":"abaac011d021fc250bf19519c4f5f87192e0a790","after":"43a8ccf6c426cd3584f91b1b7cf1d0ea9f54f06c","ref":"refs/heads/background","pushedAt":"2024-02-01T00:34:19.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"refactor: purge columns from memory","shortMessageHtmlLink":"refactor: purge columns from memory"}},{"before":"6a8c0420c0ecdf7ee2a67a096f03329239452140","after":"abaac011d021fc250bf19519c4f5f87192e0a790","ref":"refs/heads/background","pushedAt":"2024-01-31T21:30:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"refactor: replace `utils.to_feature_matrix` -> `np.vstack`","shortMessageHtmlLink":"refactor: replace utils.to_feature_matrix -> np.vstack"}},{"before":"46b526c0bb6fc1f5c23c49c71946c2696e627c8f","after":"8db7a279a504030f75f3788ddb1e9ced3ff1eca4","ref":"refs/heads/functionmotifs","pushedAt":"2024-01-30T18:34:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tnitka","name":"Tara A. Nitka","path":"/tnitka","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/86532598?s=80&v=4"},"commit":{"message":"Add Motif tutorial","shortMessageHtmlLink":"Add Motif tutorial"}},{"before":"60fb8d2f6926287ba0a116adf84ad19354737e5d","after":"6a8c0420c0ecdf7ee2a67a096f03329239452140","ref":"refs/heads/background","pushedAt":"2024-01-30T18:20:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"fix: use background weight config spec for scoring","shortMessageHtmlLink":"fix: use background weight config spec for scoring"}},{"before":"5522abe46598816be8e032fe279c8078289cb2f3","after":"2c2db4b17d68764d229920287283392c9b3dc743","ref":"refs/heads/kmer-association","pushedAt":"2024-01-25T18:56:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jjacobson95","name":"Jeremy Jacobson","path":"/jjacobson95","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85139244?s=80&v=4"},"commit":{"message":"Update requirements.txt","shortMessageHtmlLink":"Update requirements.txt"}},{"before":"e8316e21a587d3255ddc6e1b79c95176921852a3","after":"5522abe46598816be8e032fe279c8078289cb2f3","ref":"refs/heads/kmer-association","pushedAt":"2024-01-25T04:10:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jjacobson95","name":"Jeremy Jacobson","path":"/jjacobson95","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85139244?s=80&v=4"},"commit":{"message":"Update setup.py","shortMessageHtmlLink":"Update setup.py"}},{"before":"aedbc58075cc65f3494d2c6e88c6ed78b7be44a7","after":"e8316e21a587d3255ddc6e1b79c95176921852a3","ref":"refs/heads/kmer-association","pushedAt":"2024-01-25T04:03:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jjacobson95","name":"Jeremy Jacobson","path":"/jjacobson95","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85139244?s=80&v=4"},"commit":{"message":"Update setup.py","shortMessageHtmlLink":"Update setup.py"}},{"before":"5579c7f0d598a6a636c650112e052efaa483276a","after":"aedbc58075cc65f3494d2c6e88c6ed78b7be44a7","ref":"refs/heads/kmer-association","pushedAt":"2024-01-25T04:01:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jjacobson95","name":"Jeremy Jacobson","path":"/jjacobson95","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85139244?s=80&v=4"},"commit":{"message":"Update setup.py","shortMessageHtmlLink":"Update setup.py"}},{"before":"4c9a71d3cca57fc3cbc0cf265134ecfea61d899b","after":"60fb8d2f6926287ba0a116adf84ad19354737e5d","ref":"refs/heads/background","pushedAt":"2024-01-09T00:38:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinehc","name":"Christine Chang","path":"/christinehc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/46230556?s=80&v=4"},"commit":{"message":"fix,style: update search file glob. apply snakefmt\n\nchangelog:\n- fix: search file globbing updated to use snakemake's `glob_wildcards` rather than python's `glob.glob` in search mode. Should also resolve issues with file detection for files requiring unzipping and avoid recursion errors. Tested locally with a small subset of small families.\n- style: applied snakefmt to `cluster.smk` and `search.smk`","shortMessageHtmlLink":"fix,style: update search file glob. apply snakefmt"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAERtaeAQA","startCursor":null,"endCursor":null}},"title":"Activity · PNNL-CompBio/Snekmer"}