{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":526720049,"defaultBranch":"main","name":"wsinfer","ownerLogin":"SBU-BMI","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-08-19T18:53:46.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/9609848?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1720669486.0","currentOid":""},"activityList":{"items":[{"before":"5b1ac8bbf89f02840735a82811f80a8eabf110d5","after":null,"ref":"refs/heads/fix/read-mpp-with-backend","pushedAt":"2024-07-11T03:44:46.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"}},{"before":"386a2a724964a4eb018b4e72579bcd0bf5a026c7","after":"06ef6b8bd56c3ab903760c505a654ce4c2a768f9","ref":"refs/heads/main","pushedAt":"2024-07-11T03:44:43.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"only use specified backend (or tifffile) to read mpp (#227)\n\nPreviously, even if tiffslide was the chosen backend, openslide\r\nwould still be used first to get mpp. This could cause panics\r\nif a slide could not be read by openslide. This panic could\r\nconfuse users because they asked to use tiffslide. This commit\r\nchanges the mpp reading function to use the chosen backend or\r\ntifffile if that backend fails.","shortMessageHtmlLink":"only use specified backend (or tifffile) to read mpp (#227)"}},{"before":null,"after":"5b1ac8bbf89f02840735a82811f80a8eabf110d5","ref":"refs/heads/fix/read-mpp-with-backend","pushedAt":"2024-07-10T22:30:18.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"only use specified backend (or tifffile) to read mpp\n\nPreviously, even if tiffslide was the chosen backend, openslide\nwould still be used first to get mpp. This could cause panics\nif a slide could not be read by openslide. This panic could\nconfuse users because they asked to use tiffslide. This commit\nchanges the mpp reading function to use the chosen backend or\ntifffile if that backend fails.","shortMessageHtmlLink":"only use specified backend (or tifffile) to read mpp"}},{"before":"333973356f1e7aa5633576e71869ef755749f93b","after":null,"ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T22:18:06.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"}},{"before":"ff796954017f79769c813d6b4d619dafc57bd663","after":"386a2a724964a4eb018b4e72579bcd0bf5a026c7","ref":"refs/heads/main","pushedAt":"2024-07-10T22:18:03.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"fix backend setting (#226)\n\n* fix backend setting\r\n\r\n* format with ruff\r\n\r\n* remove zarr KVStore monkey patch\r\n\r\nTiffslide takes care of the monkeypatching for us.\r\nIncluding it here caused errors in our tests.\r\n\r\n* attempt to fix zarr.storage issue\r\n\r\n* expect 601 slides in linux and macos\r\n\r\n* expect 601 patches in docker output\r\n\r\n* install numpy, openslide, tiffslide after torch","shortMessageHtmlLink":"fix backend setting (#226)"}},{"before":"8bbf9388f97cb100ee208ef51dd3aaf14e17ee21","after":"333973356f1e7aa5633576e71869ef755749f93b","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T22:06:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"install numpy, openslide, tiffslide after torch","shortMessageHtmlLink":"install numpy, openslide, tiffslide after torch"}},{"before":"22dfe1a6bfe5bd600cbc3a78fa0b472288cecfee","after":"8bbf9388f97cb100ee208ef51dd3aaf14e17ee21","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:59:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"expect 601 patches in docker output","shortMessageHtmlLink":"expect 601 patches in docker output"}},{"before":"358451155fa4cf929582becb15ac182e08c05cff","after":"22dfe1a6bfe5bd600cbc3a78fa0b472288cecfee","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:58:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"expect 601 slides in linux and macos","shortMessageHtmlLink":"expect 601 slides in linux and macos"}},{"before":"b775194fb6f64130aef171dcf6ad5e8512c90e9e","after":"358451155fa4cf929582becb15ac182e08c05cff","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:44:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"attempt to fix zarr.storage issue","shortMessageHtmlLink":"attempt to fix zarr.storage issue"}},{"before":"7a2704392153fce551f2d8a3e458b1e397cef76d","after":"b775194fb6f64130aef171dcf6ad5e8512c90e9e","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:37:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"remove zarr KVStore monkey patch\n\nTiffslide takes care of the monkeypatching for us.\nIncluding it here caused errors in our tests.","shortMessageHtmlLink":"remove zarr KVStore monkey patch"}},{"before":"27ac8ec8b34b071350967be1001787d01dd6586d","after":"7a2704392153fce551f2d8a3e458b1e397cef76d","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:30:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"format with ruff","shortMessageHtmlLink":"format with ruff"}},{"before":null,"after":"27ac8ec8b34b071350967be1001787d01dd6586d","ref":"refs/heads/fix/issue-225","pushedAt":"2024-07-10T21:27:06.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"fix backend setting","shortMessageHtmlLink":"fix backend setting"}},{"before":"c8354f576ca5d591322f04ac5c60da13e1956f4f","after":null,"ref":"refs/heads/docs/add-academic-warning","pushedAt":"2024-07-09T18:15:52.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"}},{"before":"e1843def83d3afd6a6698154f2453799a933d5d7","after":"ff796954017f79769c813d6b4d619dafc57bd663","ref":"refs/heads/main","pushedAt":"2024-07-09T18:15:48.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"[DOC] add disclaimer that this project is for academic research purposes only (#224) [skip ci]\n\n* add academic research use warning to readme\r\n\r\n* add academic research disclaimer\r\n\r\n* update float and int types for slide coords and probs\r\n\r\nUse np.floating and np.integer.\r\n\r\n* do not ignore types when making binary im arr","shortMessageHtmlLink":"[DOC] add disclaimer that this project is for academic research purpo…"}},{"before":"385ce1f903959ea20c0a4c98cb3f66b6197c058e","after":"c8354f576ca5d591322f04ac5c60da13e1956f4f","ref":"refs/heads/docs/add-academic-warning","pushedAt":"2024-07-09T17:57:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"do not ignore types when making binary im arr","shortMessageHtmlLink":"do not ignore types when making binary im arr"}},{"before":"7a867ceaa639f1cc97b70cea8934a299132088af","after":"385ce1f903959ea20c0a4c98cb3f66b6197c058e","ref":"refs/heads/docs/add-academic-warning","pushedAt":"2024-07-09T17:55:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"update float and int types for slide coords and probs\n\nUse np.floating and np.integer.","shortMessageHtmlLink":"update float and int types for slide coords and probs"}},{"before":"6302c5960843f803559d21f40cd85ab5baf37fbb","after":"7a867ceaa639f1cc97b70cea8934a299132088af","ref":"refs/heads/docs/add-academic-warning","pushedAt":"2024-07-09T17:48:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"add academic research disclaimer","shortMessageHtmlLink":"add academic research disclaimer"}},{"before":null,"after":"6302c5960843f803559d21f40cd85ab5baf37fbb","ref":"refs/heads/docs/add-academic-warning","pushedAt":"2024-07-09T17:43:37.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"add academic research use warning to readme","shortMessageHtmlLink":"add academic research use warning to readme"}},{"before":"eebff66f1c8ddec0d05bdc838deef80fc52aa967","after":"e1843def83d3afd6a6698154f2453799a933d5d7","ref":"refs/heads/main","pushedAt":"2024-02-22T20:51:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"[skip ci] add 0.6.0 and 0.6.1 to version switcher","shortMessageHtmlLink":"[skip ci] add 0.6.0 and 0.6.1 to version switcher"}},{"before":"e07148d8064b9aba79e50c69f038e092e8382706","after":null,"ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:47:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"}},{"before":"f39f92b5c282cafcc42ca2934e17667de852b2d6","after":"eebff66f1c8ddec0d05bdc838deef80fc52aa967","ref":"refs/heads/main","pushedAt":"2024-02-22T20:47:35.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"[STYLE] use ruff in lieu of black/flake8/isort + add pre-commit (#219)\n\n* appease mypy\r\n\r\n* add ruff configs\r\n\r\n* check and format with ruff\r\n\r\n* add ruff and remove black/isort/flake8\r\n\r\n* add pre-commit and instructions\r\n\r\n* ruff ignore scripts/ + fix with ruff\r\n\r\n* install all deps for mypy + add \"all\" extra\r\n\r\n* do not check mypy in nightly pytorch","shortMessageHtmlLink":"[STYLE] use ruff in lieu of black/flake8/isort + add pre-commit (#219)"}},{"before":"e165c5482cfe05a3824950c07d7c95c2f6abc1a8","after":"e07148d8064b9aba79e50c69f038e092e8382706","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:35:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"do not check mypy in nightly pytorch","shortMessageHtmlLink":"do not check mypy in nightly pytorch"}},{"before":"421a7253d0c8d6a890892811e0eaac70fc205c79","after":"e165c5482cfe05a3824950c07d7c95c2f6abc1a8","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:31:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"install all deps for mypy + add \"all\" extra","shortMessageHtmlLink":"install all deps for mypy + add \"all\" extra"}},{"before":"c26783b4da43846176b849cd9f247229a141a0b1","after":"421a7253d0c8d6a890892811e0eaac70fc205c79","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:25:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"ruff ignore scripts/ + fix with ruff","shortMessageHtmlLink":"ruff ignore scripts/ + fix with ruff"}},{"before":"1f35a28995664eda4f4d3a48a236825064640736","after":"c26783b4da43846176b849cd9f247229a141a0b1","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:21:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"add pre-commit and instructions","shortMessageHtmlLink":"add pre-commit and instructions"}},{"before":"6290abb209096a831cea6244db66f851cdd14204","after":"1f35a28995664eda4f4d3a48a236825064640736","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:17:15.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"add ruff and remove black/isort/flake8","shortMessageHtmlLink":"add ruff and remove black/isort/flake8"}},{"before":null,"after":"6290abb209096a831cea6244db66f851cdd14204","ref":"refs/heads/sty/ruff","pushedAt":"2024-02-22T20:06:25.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"add ruff configs","shortMessageHtmlLink":"add ruff configs"}},{"before":"39d8e9d79768010898b9caf4348d098d7d4d16ff","after":null,"ref":"refs/heads/enh/cleaning-issues","pushedAt":"2024-02-22T19:34:51.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"}},{"before":"d52855ab370515f817b8f72df112afe6f4cc8a7d","after":"f39f92b5c282cafcc42ca2934e17667de852b2d6","ref":"refs/heads/main","pushedAt":"2024-02-22T19:34:49.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"Cleanup + add strided patches (#218)\n\n* rm unused args, fix #185\r\n\r\n* account for empty hierarchy or patches\r\n\r\nfix #195\r\n\r\n* please mypy\r\n\r\n* make error message more helpful if patch dir does not exist\r\n\r\n* rm unused args in wsi patches dataset\r\n\r\nfixes #185\r\n\r\n* check that there are patches in the loaded file\r\n\r\nfixes #195\r\n\r\n* ensure thumbnail is RGB\r\n\r\nfixes #216\r\n\r\n* appease mypy\r\n\r\n* test that openslide and tiffslide pad regions\r\n\r\nfixes #203\r\n\r\n* rm unused import\r\n\r\n* handle symlinked slides dirs\r\n\r\nfixes #214\r\n\r\n* add strided patches\r\n\r\nfixes #202\r\n\r\nThis adds a command line option '--patch-overlap-ratio' that controls\r\nthe level of overlap between adjacent patches. Negative values create\r\nspace between patches, and values closer to 1 makes patches overlap\r\nmore.\r\n\r\n* save jsons with geojson ext\r\n\r\n* print some logs\r\n\r\n* use geojson ext for purple.json","shortMessageHtmlLink":"Cleanup + add strided patches (#218)"}},{"before":"da971951d2ef804ba10907ab7430db6c2909c489","after":"39d8e9d79768010898b9caf4348d098d7d4d16ff","ref":"refs/heads/enh/cleaning-issues","pushedAt":"2024-02-22T19:17:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kaczmarj","name":"Jakub Kaczmarzyk","path":"/kaczmarj","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17690870?s=80&v=4"},"commit":{"message":"use geojson ext for purple.json","shortMessageHtmlLink":"use geojson ext for purple.json"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEfGMcLAA","startCursor":null,"endCursor":null}},"title":"Activity · SBU-BMI/wsinfer"}