{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":406555580,"defaultBranch":"main","name":"openfold","ownerLogin":"aqlaboratory","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-09-14T23:59:02.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/8396911?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1711651021.0","currentOid":""},"activityList":{"items":[{"before":"81c847b1738231633b061a8f2e9dbfbab9fd7d65","after":"cb3ff410c3adc8a20280b174c55879ba170e902f","ref":"refs/heads/setup-improvements","pushedAt":"2024-04-23T09:40:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"run_pretrained_openfold.py: Change default paths of binary to be conda environment bin","shortMessageHtmlLink":"run_pretrained_openfold.py: Change default paths of binary to be cond…"}},{"before":"fdd4e1d80cf6f8c2082fb1c3d86990ba5e0fdc58","after":"81c847b1738231633b061a8f2e9dbfbab9fd7d65","ref":"refs/heads/setup-improvements","pushedAt":"2024-04-22T10:05:11.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"clear up some space for docker ci","shortMessageHtmlLink":"clear up some space for docker ci"}},{"before":"732d283a96972ca5377ee9934330e14267c02f29","after":null,"ref":"refs/heads/resolution-fix","pushedAt":"2024-03-28T18:37:01.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ljarosch","name":null,"path":"/ljarosch","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69863115?s=80&v=4"}},{"before":"df8a002dc5c2536ad415afc3b6ada97e7279252c","after":"80c85b54e1a81d9a66df3f1b6c257ff97f10acd3","ref":"refs/heads/main","pushedAt":"2024-03-28T18:37:00.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"ljarosch","name":null,"path":"/ljarosch","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69863115?s=80&v=4"},"commit":{"message":"Merge pull request #420 from aqlaboratory/resolution-fix\n\nFix resolution field in mmcif_parsing","shortMessageHtmlLink":"Merge pull request #420 from aqlaboratory/resolution-fix"}},{"before":"d32c0995bf2abaefaa412e8f82ce92de25ca7c78","after":"df8a002dc5c2536ad415afc3b6ada97e7279252c","ref":"refs/heads/main","pushedAt":"2024-03-26T21:36:40.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"sachinkadyan7","name":"Sachin Kadyan","path":"/sachinkadyan7","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19634735?s=80&v=4"},"commit":{"message":"Add script to download embeddings for training SoloSeq","shortMessageHtmlLink":"Add script to download embeddings for training SoloSeq"}},{"before":"127f1e7023c380c01330cee45544c23c079babe9","after":"d32c0995bf2abaefaa412e8f82ce92de25ca7c78","ref":"refs/heads/main","pushedAt":"2024-03-26T20:16:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sachinkadyan7","name":"Sachin Kadyan","path":"/sachinkadyan7","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19634735?s=80&v=4"},"commit":{"message":"Add LICENSE information to decoy ranking script","shortMessageHtmlLink":"Add LICENSE information to decoy ranking script"}},{"before":"a56ea9b5641c86a4183b772ed9b92af794a991d4","after":null,"ref":"refs/heads/seeding-fix","pushedAt":"2024-03-21T08:41:43.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"}},{"before":"ef0c9face788001b1624b3b2dbfa951072841835","after":"127f1e7023c380c01330cee45544c23c079babe9","ref":"refs/heads/main","pushedAt":"2024-03-21T08:41:42.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Merge pull request #418 from aqlaboratory/seeding-fix\n\nFix distributed seeding behavior","shortMessageHtmlLink":"Merge pull request #418 from aqlaboratory/seeding-fix"}},{"before":"6ba0a594c9d2caedc8edf42b1215ec4dc7834a29","after":"fdd4e1d80cf6f8c2082fb1c3d86990ba5e0fdc58","ref":"refs/heads/setup-improvements","pushedAt":"2024-03-21T07:04:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"update license file","shortMessageHtmlLink":"update license file"}},{"before":null,"after":"732d283a96972ca5377ee9934330e14267c02f29","ref":"refs/heads/resolution-fix","pushedAt":"2024-03-21T03:05:14.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ljarosch","name":null,"path":"/ljarosch","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69863115?s=80&v=4"},"commit":{"message":"Fix resolution field in mmcif_parsing\n\nWithout the break statement this function will fall back to setting the resolution to _reflns.d_resolution_high for most structures, which reflects the resolution limit in the raw data and not the final structure (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html and https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html).","shortMessageHtmlLink":"Fix resolution field in mmcif_parsing"}},{"before":null,"after":"94819bf136cb7cfa57133a5d190c582840502f1c","ref":"refs/heads/setup-improvements_additional-scripts","pushedAt":"2024-03-20T04:04:39.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ljarosch","name":null,"path":"/ljarosch","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69863115?s=80&v=4"},"commit":{"message":"Add script for expanding the alignment dir with duplicates\n\nThis adds support for duplicate chain expansion for the alignment dir format. This script can be run on the flattened non-redundant RODA alignments to add explicit directories for all of the duplicate chains in the duplicate_chains file, symlinked to their representative chain alignment directory.","shortMessageHtmlLink":"Add script for expanding the alignment dir with duplicates"}},{"before":null,"after":"a56ea9b5641c86a4183b772ed9b92af794a991d4","ref":"refs/heads/seeding-fix","pushedAt":"2024-03-19T17:05:27.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ljarosch","name":null,"path":"/ljarosch","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69863115?s=80&v=4"},"commit":{"message":"Fix distributed seeding behavior\n\nThis adds workers=True to the Lightning seed_everything function which guarantees different random states across all processes in distributed training. Prior to that some processes on different GPUs with the same worker ID could share the same random state.\n\nNote that this will break reproducibility between runs prior to and after this change.\n\nAlso removes the seed and supress_output modules that were not used anymore in OpenFold.","shortMessageHtmlLink":"Fix distributed seeding behavior"}},{"before":"f4df72173d7b3a6d3667cdc5e849649c79c0c6c8","after":"6ba0a594c9d2caedc8edf42b1215ec4dc7834a29","ref":"refs/heads/setup-improvements","pushedAt":"2024-03-13T06:00:01.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"adds config recording to wandb","shortMessageHtmlLink":"adds config recording to wandb"}},{"before":"ed40380c76f2836dc2ff1ebe20231b3df2b005fc","after":"ef0c9face788001b1624b3b2dbfa951072841835","ref":"refs/heads/main","pushedAt":"2024-02-26T06:52:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sachinkadyan7","name":"Sachin Kadyan","path":"/sachinkadyan7","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19634735?s=80&v=4"},"commit":{"message":"Added script for running decoy ranking experiments","shortMessageHtmlLink":"Added script for running decoy ranking experiments"}},{"before":"bb3f51e5a2cf2d5e3b709fe8f7d7a083c870222e","after":"ed40380c76f2836dc2ff1ebe20231b3df2b005fc","ref":"refs/heads/main","pushedAt":"2024-02-23T19:18:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"},"commit":{"message":"Hotfix to switch order of feature dict generation","shortMessageHtmlLink":"Hotfix to switch order of feature dict generation"}},{"before":"f1cd1381528a773fa83bcb571f5778dc3a14c000","after":"f4df72173d7b3a6d3667cdc5e849649c79c0c6c8","ref":"refs/heads/setup-improvements","pushedAt":"2024-02-22T09:03:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.","shortMessageHtmlLink":"Changes resume_model_weights_only flag in train_openfold to reload we…"}},{"before":"9776b696343cfb55f058d5de7e76d343981f3fdd","after":"f1cd1381528a773fa83bcb571f5778dc3a14c000","ref":"refs/heads/setup-improvements","pushedAt":"2024-02-21T07:39:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"removes outputs from OpenFold.ipynb","shortMessageHtmlLink":"removes outputs from OpenFold.ipynb"}},{"before":"119529972ebb030e8b4f27fbef2cb141e8841662","after":"9776b696343cfb55f058d5de7e76d343981f3fdd","ref":"refs/heads/setup-improvements","pushedAt":"2024-02-21T07:06:55.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Merge weight-loading changes into setup-improvements","shortMessageHtmlLink":"Merge weight-loading changes into setup-improvements"}},{"before":"a3bb3c40c7a759a60c468d2502ab9204ac7074a0","after":"119529972ebb030e8b4f27fbef2cb141e8841662","ref":"refs/heads/setup-improvements","pushedAt":"2024-02-20T17:32:27.000Z","pushType":"push","commitsCount":415,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"},"commit":{"message":"Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements","shortMessageHtmlLink":"Merge branch 'setup-improvements' of https://github.com/aqlaboratory/…"}},{"before":"df4dfacb3aade38f1d222c0902485c35a358f64a","after":"49ab0539547b9ae921d8bc7c2beb106e085fc3cf","ref":"refs/heads/pl_upgrades","pushedAt":"2024-02-19T08:35:43.000Z","pushType":"pr_merge","commitsCount":36,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Merge pull request #407 from jnwei/pl_upgrades\n\nPytorch lightning upgrades","shortMessageHtmlLink":"Merge pull request #407 from jnwei/pl_upgrades"}},{"before":"e2e19f16676b1a409f9ba3a6f69b11ee7f5887c2","after":"a96ffd67f8c96f8c4decc3abdd2cffbb57fc5764","ref":"refs/heads/multimer-colab-patch","pushedAt":"2024-02-15T15:12:21.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Bump actions/setup-python from 4 to 5\n\nBumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.\n- [Release notes](https://github.com/actions/setup-python/releases)\n- [Commits](https://github.com/actions/setup-python/compare/v4...v5)\n\n---\nupdated-dependencies:\n- dependency-name: actions/setup-python\n dependency-type: direct:production\n update-type: version-update:semver-major\n...\n\nSigned-off-by: dependabot[bot] ","shortMessageHtmlLink":"Bump actions/setup-python from 4 to 5"}},{"before":"15eefcc16f1b49931569d0c3afb6e67a813e0e6f","after":null,"ref":"refs/heads/chunking_experiment","pushedAt":"2024-02-08T09:31:24.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"}},{"before":"5c1fc2d2a8170443a5f4f56796fd6b43984e0169","after":null,"ref":"refs/heads/mpvenkatesh/changes","pushedAt":"2024-02-08T09:31:23.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"}},{"before":"59cb94876a9c8a248ee186fdc5876e72b0bddb4d","after":null,"ref":"refs/heads/chunking_experiment_2","pushedAt":"2024-02-08T09:28:43.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"}},{"before":"ce21136785b1c71e4fb8da10190789611c3e21b2","after":"bb3f51e5a2cf2d5e3b709fe8f7d7a083c870222e","ref":"refs/heads/main","pushedAt":"2024-02-08T04:06:08.000Z","pushType":"pr_merge","commitsCount":282,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"},"commit":{"message":"Merge pull request #405 from aqlaboratory/multimer\n\nFull multimer merge","shortMessageHtmlLink":"Merge pull request #405 from aqlaboratory/multimer"}},{"before":"c33a0bd68ee3522b20d5f8fdef30080b4af5d910","after":null,"ref":"refs/heads/multimer","pushedAt":"2024-02-08T04:06:08.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"}},{"before":"6275091c962f90847907b68e5f205b1866fde2d3","after":"c33a0bd68ee3522b20d5f8fdef30080b4af5d910","ref":"refs/heads/multimer","pushedAt":"2024-02-07T20:48:08.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"},"commit":{"message":"Merge branch 'main' into multimer","shortMessageHtmlLink":"Merge branch 'main' into multimer"}},{"before":"bc07500422aa99343d4fa95efd6eb3860301db59","after":"6275091c962f90847907b68e5f205b1866fde2d3","ref":"refs/heads/multimer","pushedAt":"2024-02-07T20:47:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"christinaflo","name":"Christina Floristean","path":"/christinaflo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22804099?s=80&v=4"},"commit":{"message":"Fixed learning rate scheduler issue, returned to original msa file parsing","shortMessageHtmlLink":"Fixed learning rate scheduler issue, returned to original msa file pa…"}},{"before":"5e0616b641af4aa25134e8aa9761afa929153ca1","after":"bc07500422aa99343d4fa95efd6eb3860301db59","ref":"refs/heads/multimer","pushedAt":"2024-02-07T16:25:00.000Z","pushType":"pr_merge","commitsCount":21,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"},"commit":{"message":"Merge pull request #404 from jnwei/multimer-small-edits\n\nType fixes and README changes for multimer branch","shortMessageHtmlLink":"Merge pull request #404 from jnwei/multimer-small-edits"}},{"before":"111704b18315849ae299178c329bb1cb02632f24","after":null,"ref":"refs/heads/multimer-notebook","pushedAt":"2024-02-07T15:57:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"jnwei","name":"Jennifer Wei","path":"/jnwei","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/97625454?s=80&v=4"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEN-RLXAA","startCursor":null,"endCursor":null}},"title":"Activity · aqlaboratory/openfold"}