{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":15168264,"defaultBranch":"main","name":"scikit-bio","ownerLogin":"scikit-bio","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2013-12-13T16:24:41.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/121500820?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1716584837.0","currentOid":""},"activityList":{"items":[{"before":"094b166eeb77805a5501df862874c3f67c25428d","after":"e1ede1e3b4e729f5a6d136cd5cf7f157f3520049","ref":"refs/heads/main","pushedAt":"2024-06-01T14:43:24.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Minor edits of embedding (#2031)\n\n* minor edits of embedding\r\n\r\n* upped embed\r\n\r\n* fixing embed\r\n\r\n* additional fixes\r\n\r\n* minor edits to unit-test\r\n\r\n* added init\r\n\r\n* included test file","shortMessageHtmlLink":"Minor edits of embedding (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2324916023\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2031\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2031/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2031\">#2031</a>)"}},{"before":"c1d6c1853f9422378678a451856aaf631ab1ea06","after":"094b166eeb77805a5501df862874c3f67c25428d","ref":"refs/heads/main","pushedAt":"2024-05-31T06:18:31.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Replace _subsample with biom's optimized subsample (#2016)\n\n* Replace _subsample with biom's optimized subsample\r\n\r\n* comment on inplace operation:\r\n\r\n* Remove subsample from setup\r\n\r\n* MAINT: update import\r\n\r\n* BLD: pin biom-format for subsample import\r\n\r\n* DOC: changelog mention of subsample change\r\n\r\n* Address @qiyunzhu's comment\r\n\r\n* CI: use OSX x86_64 and M1\r\n\r\n* value clarity\r\n\r\n* See if we're just unlucky","shortMessageHtmlLink":"Replace _subsample with biom's optimized subsample (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2274007724\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2016\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2016/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2016\">#2016</a>)"}},{"before":"1ca386a7bd7a52f15c7ff2b93dd9b976793dfe00","after":"c1d6c1853f9422378678a451856aaf631ab1ea06","ref":"refs/heads/main","pushedAt":"2024-05-29T17:27:08.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Efficient sequence alignment path data structure (#2011)\n\n* initial commit\r\n\r\n* add path function to tabularMSA and create util file\r\n\r\n* Add _util.py file\r\n\r\n* Add basic to_cigar and from_cigar functions\r\n\r\n* Start unit tests for PairAlignPath\r\n\r\n* Add ability to handle = or X to from_cigar function\r\n\r\n* Add code attribution for part taken from SO\r\n\r\n* Remove print statement\r\n\r\n* Initial version of handling match vs mismatch for to_cigar\r\n\r\n* Split encoding into separate function\r\n\r\n* Change input name\r\n\r\n* Add test data\r\n\r\n* Start on unit tests\r\n\r\n* Update fix_arrays function\r\n\r\n* Change from np.nan to 0 for append in fix_arrays\r\n\r\n* Numpy version of run_length_encode\r\n\r\n* Fix fix_arrays function\r\n\r\n* Enable from_cigar to handle strings with or without ones\r\n\r\n* Add error handling and tests for from_bits in PairAlign\r\n\r\n* PairAlignPath fully covered\r\n\r\n* Expand unit tests\r\n\r\n* Test more than 8 seqs for from_bits\r\n\r\n* To_indices tests\r\n\r\n* Complete coverage for to_indices\r\n\r\n* Full coverage\r\n\r\n* Update init file\r\n\r\n* Added non default gap character handling to from_tabular\r\n\r\n* Add skbioobject to class\r\n\r\n* Update fix_arrays\r\n\r\n* Basic repr function\r\n\r\n* Switch to starts from n_seqs\r\n\r\n* Rewrite unit tests\r\n\r\n* Remove large data files\r\n\r\n* Simplify pairwise_align_score\r\n\r\n* Docstring as raw strings and fix toctree\r\n\r\n* Simplify pairwise align_score and rename multiple_align_scores\r\n\r\n* Fix tabular from_path_seqs\r\n\r\n* Improve docstrings\r\n\r\n* Change to np.int64 to make Windows compatible\r\n\r\n* Remove alignment score functions for future PR\r\n\r\n* Allow for non numpy array like in from_bits\r\n\r\n* Remove overrides decorator, see what happens\r\n\r\n* Finish docstrings for PairAlignPath\r\n\r\n* Remove unused import\r\n\r\n* Improve error handling for to_cigar and remove subset\r\n\r\n* Improve error handling for to_cigar\r\n\r\n* Figuring out to_cigar\r\n\r\n* Fix to_cigar functionality by converting to str\r\n\r\n* Complete unit tests for to_cigar\r\n\r\n* Finish unit test for from_cigar\r\n\r\n* Unit tests for initialization\r\n\r\n* Modify Pair to_bits to handle two gaps\r\n\r\n* Functional version of to_cigar\r\n\r\n* Enhanced to_cigar function\r\n\r\n* Remove gap chars for to_cigar\r\n\r\n* Enhancement comments\r\n\r\n* Modify to_cigar logic\r\n\r\n* Optimized version of to_cigar\r\n\r\n* Update docstrings\r\n\r\n* Update unittests\r\n\r\n* Test RLE\r\n\r\n* Add Tabular from_path_seqs test\r\n\r\n* Remove float option for gap in to_indices\r\n\r\n* Update CHANGELOG\r\n\r\n* Address most recent comments\r\n\r\n* Move mapping and switch to unsigned int for starts\r\n\r\n* Rename mapping and codes\r\n\r\n* Create class properties for states, starts, lengths, and shapes\r\n\r\n* Switch ValueError to TypeError where appropriate\r\n\r\n* Paired programming additions\r\n\r\n* Update to/from_indices functionality to handle starts\r\n\r\n* Update to/from_coordinates functionality to handle starts\r\n\r\n* Lint tests\r\n\r\n* Remove unused import\r\n\r\n* Start on docstring examples\r\n\r\n* AlignPath docstring\r\n\r\n* Add examples to docstrings\r\n\r\n* Add example text\r\n\r\n* More examples\r\n\r\n* Final examples\r\n\r\n* Change gaps to starts\r\n\r\n* Fix doctests","shortMessageHtmlLink":"Efficient sequence alignment path data structure (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2251102131\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2011\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2011/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2011\">#2011</a>)"}},{"before":"541a9305da50ffc606cb6107385676622f2486a8","after":"1ca386a7bd7a52f15c7ff2b93dd9b976793dfe00","ref":"refs/heads/main","pushedAt":"2024-05-28T04:39:59.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"fix typo in link to Github repository (#2030)","shortMessageHtmlLink":"fix typo in link to Github repository (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2320013292\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2030\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2030/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2030\">#2030</a>)"}},{"before":"3faea7e9b81c8c7ad13ef747abecac4d97f79d6c","after":null,"ref":"refs/heads/qiyunzhu-patch-1","pushedAt":"2024-05-24T21:07:17.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"}},{"before":"7eedaf58b8f80c6c90aa363857d1dca160071423","after":"541a9305da50ffc606cb6107385676622f2486a8","ref":"refs/heads/main","pushedAt":"2024-05-24T21:06:55.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Protein Vector object (#2021)\n\n* first iteration of protein vector object\r\n\r\n* linter\r\n\r\n* renaming files to see if it improves coverage\r\n\r\n* improving coverage\r\n\r\n* updating coveragerc to determine if tests are being run\r\n\r\n* revert and update docs\r\n\r\n* revert typo\r\n\r\n* Update skbio/io/format/embed.py\r\n\r\nCo-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>\r\n\r\n* Update skbio/io/format/embed.py\r\n\r\nCo-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>\r\n\r\n* Update skbio/io/format/embed.py\r\n\r\nCo-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>\r\n\r\n* Update skbio/io/format/embed.py\r\n\r\nCo-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>\r\n\r\n* Update skbio/embedding/_embedding.py\r\n\r\n* address @wasade comments\r\n\r\n* address more comments\r\n\r\n* simplifying validate check\r\n\r\n* adding extra check for validation in SequenceVector\r\n\r\n* adding svd test\r\n\r\n* address comments\r\n\r\n* reverting embedding comment\r\n\r\n---------\r\n\r\nCo-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>","shortMessageHtmlLink":"Protein Vector object (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2280114728\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2021\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2021/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2021\">#2021</a>)"}},{"before":null,"after":"3faea7e9b81c8c7ad13ef747abecac4d97f79d6c","ref":"refs/heads/qiyunzhu-patch-1","pushedAt":"2024-05-24T17:31:42.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"Update index.rst","shortMessageHtmlLink":"Update index.rst"}},{"before":"3faea7e9b81c8c7ad13ef747abecac4d97f79d6c","after":null,"ref":"refs/heads/qiyunzhu-patch-1","pushedAt":"2024-05-24T17:31:23.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"}},{"before":"e3a27f56970fded68ba7561767cec41e47ba3c78","after":"7eedaf58b8f80c6c90aa363857d1dca160071423","ref":"refs/heads/main","pushedAt":"2024-05-24T17:31:12.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"Update index.rst (#2028)","shortMessageHtmlLink":"Update index.rst (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2315755043\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2028\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2028/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2028\">#2028</a>)"}},{"before":null,"after":"3faea7e9b81c8c7ad13ef747abecac4d97f79d6c","ref":"refs/heads/qiyunzhu-patch-1","pushedAt":"2024-05-24T16:05:00.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Update index.rst","shortMessageHtmlLink":"Update index.rst"}},{"before":"264709e8bd28a9662f4b12bbdee776a8b64a6a71","after":"e3a27f56970fded68ba7561767cec41e47ba3c78","ref":"refs/heads/main","pushedAt":"2024-05-05T15:47:55.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"WIP : Embedding format (#2008)\n\n* adding first dirichilet mulitinomial ttest\r\n\r\n* updating tests to pass\r\n\r\n* fix tests.\r\n\r\n* updating documentation regarding confidence intervals\r\n\r\n* adding index test\r\n\r\n* adding example code\r\n\r\n* fixing bugs in dirmult\r\n\r\n* adding support for random seeds\r\n\r\n* adding more documentation regarding depth\r\n\r\n* fix ruff and doctest\r\n\r\n* doctests now pass\r\n\r\n* remove statsmodels dep\r\n\r\n* remove multipletests import\r\n\r\n* setting seed to None\r\n\r\n* adding back fudge factor\r\n\r\n* removing extra reference in doctest\r\n\r\n* whatever, at least I'm able to commit\r\n\r\n* relaxing ruff\r\n\r\n* confirm that writes are consistent with reads\r\n\r\n* fixed typo in write\r\n\r\n* fix idptr in generator\r\n\r\n* generator tests now pass\r\n\r\n* adding more functionality\r\n\r\n* including generator example\r\n\r\n* updating changelog and formatting doc\r\n\r\n* formatting example files\r\n\r\n* fixing doc rewiring\r\n\r\n* adding sequence property\r\n\r\n* adding assert test\r\n\r\n* adding test to remove spaces\r\n\r\n* example protein now has random matrix\r\n\r\n* Update skbio/embedding/_protein.py\r\n\r\n* address comments\r\n\r\n* fix doctest error\r\n\r\n* BUG: use matrix python version (#2015)\r\n\r\n* Fix trivial Windows support issues (#2005)\r\n\r\n* Initial int_ fixes\r\n\r\n* Fix permission errors\r\n\r\n* linesep fixes\r\n\r\n* Fix test_tabular_msa\r\n\r\n* Fix int32 out of range errors\r\n\r\n* Improve lladser from casting error to buffer dtype mismatch\r\n\r\n* Fix degap tests for grammared sequence\r\n\r\n* Fix dtype issues for sequence tests\r\n\r\n* Fix all errors in test_sequence\r\n\r\n* Fix errors in metadata test_missing\r\n\r\n* Fixed line ending issues in io\r\n\r\n* Change formatting\r\n\r\n* Fix more line separator issues in io/util\r\n\r\n* Fix open encoding issue\r\n\r\n* update docs\r\n\r\n* more doc updates\r\n\r\n* resolved outstanding comments\r\n\r\n* better coverage\r\n\r\n* thanks ruff\r\n\r\n* updating property doc strings\r\n\r\n* remove not implemented error\r\n\r\n* lint\r\n\r\n* adding back str\r\n\r\n* Decreasing code coverage target to 80%\r\n\r\n* closing the gap in codecov\r\n\r\n* codecov project is also 80%\r\n\r\n---------\r\n\r\nCo-authored-by: Daniel McDonald <danielmcdonald@ucsd.edu>\r\nCo-authored-by: Matt Aton <matthewaton2@gmail.com>","shortMessageHtmlLink":"WIP : Embedding format (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2240753014\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2008\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2008/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2008\">#2008</a>)"}},{"before":"0a9fc577ebf7ce894e3b3b67e5b3a5cb732076c5","after":"264709e8bd28a9662f4b12bbdee776a8b64a6a71","ref":"refs/heads/main","pushedAt":"2024-05-02T01:42:14.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Fix trivial Windows support issues (#2005)\n\n* Initial int_ fixes\r\n\r\n* Fix permission errors\r\n\r\n* linesep fixes\r\n\r\n* Fix test_tabular_msa\r\n\r\n* Fix int32 out of range errors\r\n\r\n* Improve lladser from casting error to buffer dtype mismatch\r\n\r\n* Fix degap tests for grammared sequence\r\n\r\n* Fix dtype issues for sequence tests\r\n\r\n* Fix all errors in test_sequence\r\n\r\n* Fix errors in metadata test_missing\r\n\r\n* Fixed line ending issues in io\r\n\r\n* Change formatting\r\n\r\n* Fix more line separator issues in io/util\r\n\r\n* Fix open encoding issue","shortMessageHtmlLink":"Fix trivial Windows support issues (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2234330811\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2005\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2005/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2005\">#2005</a>)"}},{"before":"3510d4bfd53aa61811502296483713fff564c3b9","after":"0a9fc577ebf7ce894e3b3b67e5b3a5cb732076c5","ref":"refs/heads/main","pushedAt":"2024-04-30T22:10:06.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"BUG: use matrix python version (#2015)","shortMessageHtmlLink":"BUG: use matrix python version (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2272450941\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2015\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2015/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2015\">#2015</a>)"}},{"before":"d59fd2f04a83d769aeb64beab3af9174520824b9","after":"3510d4bfd53aa61811502296483713fff564c3b9","ref":"refs/heads/main","pushedAt":"2024-04-05T16:46:40.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Remove all hdmedians imports and requirements (#2004)","shortMessageHtmlLink":"Remove all hdmedians imports and requirements (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2226276427\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2004\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2004/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2004\">#2004</a>)"}},{"before":"df5d62adf2eb7c8e505da5bb20ad043ffde55f05","after":"d59fd2f04a83d769aeb64beab3af9174520824b9","ref":"refs/heads/main","pushedAt":"2024-04-04T18:18:59.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"WIP:  Porting hdmedians (#2003)\n\n* Initial commit for hdmedians port\r\n\r\n* Add sum function\r\n\r\n* Remove c before cdef of main function\r\n\r\n* Add license and move imports and data defs to top of file\r\n\r\n* Remove float32 support\r\n\r\n* Revert to original design and update unit test\r\n\r\n* Remove unused hdmedians imports","shortMessageHtmlLink":"WIP: Porting hdmedians (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2223618302\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2003\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2003/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2003\">#2003</a>)"}},{"before":"4021925a72aa4d13b6a05cc152207f3ecf4c6a90","after":"df5d62adf2eb7c8e505da5bb20ad043ffde55f05","ref":"refs/heads/main","pushedAt":"2024-03-28T20:46:38.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"upped version to 0.6.1-dev (#2002)","shortMessageHtmlLink":"upped version to 0.6.1-dev (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2213872160\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2002\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2002/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2002\">#2002</a>)"}},{"before":"9cc83715d1072475434dc108c2f9e1ad0e02361b","after":"4021925a72aa4d13b6a05cc152207f3ecf4c6a90","ref":"refs/heads/main","pushedAt":"2024-03-28T00:33:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Update release.yml\n\nFinishing up","shortMessageHtmlLink":"Update release.yml"}},{"before":"c8461d40862cdc77534555e1d899a7a8f6fa35c7","after":"9cc83715d1072475434dc108c2f9e1ad0e02361b","ref":"refs/heads/main","pushedAt":"2024-03-28T00:30:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Update release.yml\n\nKeep going","shortMessageHtmlLink":"Update release.yml"}},{"before":"c9be1a24962f66ba4d5976f7b81348d1a1ea326d","after":"c8461d40862cdc77534555e1d899a7a8f6fa35c7","ref":"refs/heads/main","pushedAt":"2024-03-28T00:25:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Update release.yml\n\nTrying to get release workflow running...","shortMessageHtmlLink":"Update release.yml"}},{"before":"caf13c1e1084b5476871447e48504e883089f119","after":"c9be1a24962f66ba4d5976f7b81348d1a1ea326d","ref":"refs/heads/main","pushedAt":"2024-03-27T23:39:29.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"release 0.6.0 (#2000)","shortMessageHtmlLink":"release 0.6.0 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2212042662\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/2000\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/2000/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/2000\">#2000</a>)"}},{"before":"3e022f854132472ed158be6bd0c04a036a41f69d","after":"caf13c1e1084b5476871447e48504e883089f119","ref":"refs/heads/main","pushedAt":"2024-03-27T22:04:17.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Organizing documentation (#1999)\n\n* removed link to api stability\r\n\r\n* updated io documentation\r\n\r\n* organized sequence and alignment documents\r\n\r\n* organized tree and statistics\r\n\r\n* working on diversity and workflow\r\n\r\n* reordered modules\r\n\r\n* worked on the rest\r\n\r\n* fixed duplicated class members display\r\n\r\n* worked on metadata document\r\n\r\n* reduced font size\r\n\r\n* more edits\r\n\r\n* fixed typo\r\n\r\n* fixed readme badges","shortMessageHtmlLink":"Organizing documentation (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2211701107\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1999\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1999/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1999\">#1999</a>)"}},{"before":"f521c1ec12160fa0cc24d9791267c30d9b63e5ab","after":"3e022f854132472ed158be6bd0c04a036a41f69d","ref":"refs/heads/main","pushedAt":"2024-03-27T19:02:25.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Remove formatting for numpy arrays in SubstitutionMatrix (#1998)\n\n* Reverted arrays to pre-ruff formatting\r\n\r\n* Moved format off comments","shortMessageHtmlLink":"Remove formatting for numpy arrays in SubstitutionMatrix (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2211508465\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1998\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1998/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1998\">#1998</a>)"}},{"before":"a2ca94a93c269295ff5e8594aa78e7d7ec303e1c","after":"f521c1ec12160fa0cc24d9791267c30d9b63e5ab","ref":"refs/heads/main","pushedAt":"2024-03-26T23:50:32.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"Renaming module `feature_table` as `table` (#1997)\n\n* renamed feature_table as table\r\n\r\n* added table to documentation\r\n\r\n* fixed docstring format","shortMessageHtmlLink":"Renaming module <code>feature_table</code> as <code>table</code> (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2209473626\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1997\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1997/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1997\">#1997</a>)"}},{"before":"0c5a1090aaf6763e90a83886a9a8106e83887b99","after":"a2ca94a93c269295ff5e8594aa78e7d7ec303e1c","ref":"refs/heads/main","pushedAt":"2024-03-26T22:21:58.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Use os.remove to remove generated .biom file (#1994)\n\n* Use os.remove to remove generated .biom file\r\n\r\n* Fix documentation issues and rewrite test\r\n\r\n* BytesIO solution\r\n\r\n* Final solution using ellipsis","shortMessageHtmlLink":"Use os.remove to remove generated .biom file (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2206801463\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1994\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1994/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1994\">#1994</a>)"}},{"before":"4d14ad0cf539e8216c4335c8828b4a5973ce2121","after":"0c5a1090aaf6763e90a83886a9a8106e83887b99","ref":"refs/heads/main","pushedAt":"2024-03-26T19:12:42.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"Removing all instances of artifact (#1995)\n\n* removing all instances of artifact\r\n\r\n* thanks ruff","shortMessageHtmlLink":"Removing all instances of artifact (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2206993339\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1995\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1995/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1995\">#1995</a>)"}},{"before":"4891a54569f5a2031b0951094513696f124bf1b9","after":"4d14ad0cf539e8216c4335c8828b4a5973ce2121","ref":"refs/heads/main","pushedAt":"2024-03-22T18:32:54.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mataton","name":"Matt Aton","path":"/mataton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/62309966?s=80&v=4"},"commit":{"message":"House keeping works for the composition module (#1988)\n\n* improved composition\r\n\r\n* minor fixes\r\n\r\n* edited changelog\r\n\r\n* fixed unit test\r\n\r\n* minor fixes","shortMessageHtmlLink":"House keeping works for the composition module (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2200810488\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1988\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1988/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1988\">#1988</a>)"}},{"before":"3fb72e437841e01690a02d44a35c290953ff12d1","after":"4891a54569f5a2031b0951094513696f124bf1b9","ref":"refs/heads/main","pushedAt":"2024-03-21T20:52:23.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Fix doc rendering issues in sample_metadata (#1989)","shortMessageHtmlLink":"Fix doc rendering issues in sample_metadata (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2200998469\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1989\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1989/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1989\">#1989</a>)"}},{"before":"6eef26ca363fbcde224385e31bb0241098229279","after":"3fb72e437841e01690a02d44a35c290953ff12d1","ref":"refs/heads/main","pushedAt":"2024-03-21T03:39:53.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"Create deprecation warning function (#1987)","shortMessageHtmlLink":"Create deprecation warning function (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2198825976\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1987\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1987/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1987\">#1987</a>)"}},{"before":"9e63c0204c6b2c6357ff9a528f3eec0e7da02afa","after":"6eef26ca363fbcde224385e31bb0241098229279","ref":"refs/heads/main","pushedAt":"2024-03-20T22:23:20.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"DOC: Table mention in drivers (#1986)","shortMessageHtmlLink":"DOC: Table mention in drivers (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2198600724\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1986\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1986/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1986\">#1986</a>)"}},{"before":"bdc17dd46e2bc42f0bd50158727d72bb6acab78a","after":"9e63c0204c6b2c6357ff9a528f3eec0e7da02afa","ref":"refs/heads/main","pushedAt":"2024-03-20T19:36:02.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"qiyunzhu","name":"Qiyun Zhu","path":"/qiyunzhu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4396343?s=80&v=4"},"commit":{"message":"ENH: biom-format IO support (#1984)\n\n* ENH: biom-format IO support\r\n\r\n* DOC: example and changelog\r\n\r\n* TST: conversion support test for diversity drivers\r\n\r\n* ENH: private conversion from table to dense to support driver interoperability:\r\n\r\n* TST: alpha_diversity tests for Table conversions\r\n\r\n* ENH: alpha_diversity driver support for table\r\n\r\n* doctest output missing:\r\n\r\n* refactor, shift support logic to _util\r\n\r\n* Converstion and error checks for beta_diversity for table\r\n\r\n* ENH: table support with the beta_diversity driver\r\n\r\n* DOC: driver support mention\r\n\r\n* code coverage, fix inappropriate raise","shortMessageHtmlLink":"ENH: biom-format IO support (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2197880236\" data-permission-text=\"Title is private\" data-url=\"https://github.com/scikit-bio/scikit-bio/issues/1984\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/scikit-bio/scikit-bio/pull/1984/hovercard\" href=\"https://github.com/scikit-bio/scikit-bio/pull/1984\">#1984</a>)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEWcRn_AA","startCursor":null,"endCursor":null}},"title":"Activity · scikit-bio/scikit-bio"}