{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":557813166,"defaultBranch":"main","name":"bentopy","ownerLogin":"marrink-lab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-10-26T10:58:29.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/33900610?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1718730843.0","currentOid":""},"activityList":{"items":[{"before":"6fc8e07f3226ac50bc201598c6fa982e043ec56c","after":"04fce64b61c1f239883e6f857a69d638f7ad448c","ref":"refs/heads/rewrite","pushedAt":"2024-06-25T11:59:43.000Z","pushType":"push","commitsCount":8,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Remove --rotations flag","shortMessageHtmlLink":"Remove --rotations flag"}},{"before":"65f73d090be7a70409fa7ff5f4c9652a15339cb1","after":"6fc8e07f3226ac50bc201598c6fa982e043ec56c","ref":"refs/heads/rewrite","pushedAt":"2024-06-25T10:59:55.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Drop the locations object after placement\n\nWe have no need for keeping it around after placing the segments, and\nsince it represents a large allocations, it seems prudent to drop it as\nsoon as possible.","shortMessageHtmlLink":"Drop the locations object after placement"}},{"before":"1bed557060a4907a87429bcb56862468a1d66397","after":"65f73d090be7a70409fa7ff5f4c9652a15339cb1","ref":"refs/heads/rewrite","pushedAt":"2024-06-20T13:50:33.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Access Mask cells through a get_unchecked\n\nSlight performance improvement. An assert at the top of the function\nguarantees we didn't mess up elsewhere.","shortMessageHtmlLink":"Access Mask cells through a get_unchecked"}},{"before":"3308f2ddd80b7f4d363ba26ac7c388962062df39","after":"1bed557060a4907a87429bcb56862468a1d66397","ref":"refs/heads/rewrite","pushedAt":"2024-06-20T12:11:40.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Remove print reporting on whether a session background was reused","shortMessageHtmlLink":"Remove print reporting on whether a session background was reused"}},{"before":"c4a8f920b3f88d96d6bbad59a890254a3e31d8af","after":"3308f2ddd80b7f4d363ba26ac7c388962062df39","ref":"refs/heads/rewrite","pushedAt":"2024-06-20T11:55:42.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Retain session background when possible and implement typestate pattern","shortMessageHtmlLink":"Retain session background when possible and implement typestate pattern"}},{"before":"2e1b2d6343fe2eb81a8607ef70d7e74cf7c18da7","after":"c4a8f920b3f88d96d6bbad59a890254a3e31d8af","ref":"refs/heads/rewrite","pushedAt":"2024-06-20T09:50:52.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Rename the `number` field in Segment to `target`\n\nThe name `target` reflects the meaning more clearly and aligns the\nwording with other sections, such as the summary.\n\nNote that while the field for `state::Segment` is now called `target`,\nthe equivalent field in `config::Segment` is still called `number`. This\nis to retain the equivalence to the structure of the input file.","shortMessageHtmlLink":"Rename the number field in Segment to target"}},{"before":null,"after":"2e1b2d6343fe2eb81a8607ef70d7e74cf7c18da7","ref":"refs/heads/rewrite","pushedAt":"2024-06-18T17:14:03.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"rewrite: Set up configuration parsing.","shortMessageHtmlLink":"rewrite: Set up configuration parsing."}},{"before":"4735e1feac5e847b41dbaf4f32ca81635d3667e7","after":"d5aae0f87381ba0d9014e3e2c3dc345fccfcc486","ref":"refs/heads/main","pushedAt":"2024-06-18T13:37:25.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Introduce a naive placement strategy before spectral packing","shortMessageHtmlLink":"pack: Introduce a naive placement strategy before spectral packing"}},{"before":"8ab3c57a3badde7e1d6d0491bdb34de731848ee3","after":"4735e1feac5e847b41dbaf4f32ca81635d3667e7","ref":"refs/heads/main","pushedAt":"2024-06-13T14:35:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Flush stdout buffer when printing after segment placement","shortMessageHtmlLink":"pack: Flush stdout buffer when printing after segment placement"}},{"before":"07d438fb24e2e8b85c66c79acb05bd691ada51b4","after":"8ab3c57a3badde7e1d6d0491bdb34de731848ee3","ref":"refs/heads/main","pushedAt":"2024-06-13T14:15:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Add a quick summary at the end of a run","shortMessageHtmlLink":"pack: Add a quick summary at the end of a run"}},{"before":"f0b24f2ee7761295b82ce67f5908f3ee530c8f8c","after":"07d438fb24e2e8b85c66c79acb05bd691ada51b4","ref":"refs/heads/main","pushedAt":"2024-06-13T12:56:38.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"voxelize: Scale the radius when checking against the scaled points\n\nThis was responsible for a 0.5× difference between expected minimum bead\ndistance between placed structure instances, and the reality.\n\nAfter this change, `bentopy check` returns the minimum distance where we\nexpect it.\n\nThanks, Jan, for letting me talk through it and pointing out the\nmistake!","shortMessageHtmlLink":"voxelize: Scale the radius when checking against the scaled points"}},{"before":"ea8196aebf83d4af1d2e859d7bed1c41c654e0d0","after":"f0b24f2ee7761295b82ce67f5908f3ee530c8f8c","ref":"refs/heads/main","pushedAt":"2024-06-13T10:14:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Remove stale density tracking and reporting","shortMessageHtmlLink":"pack: Remove stale density tracking and reporting"}},{"before":"cface5509d48829de21c76ff4ab2f23174533bee","after":"ea8196aebf83d4af1d2e859d7bed1c41c654e0d0","ref":"refs/heads/main","pushedAt":"2024-06-12T12:43:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Show progress count in packing log","shortMessageHtmlLink":"pack: Show progress count in packing log"}},{"before":"1bccc294cab557068d184ac27c4396ac9fcfd615","after":"cface5509d48829de21c76ff4ab2f23174533bee","ref":"refs/heads/main","pushedAt":"2024-06-12T12:17:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"voxelization: Fix three beads at axactly the axis-zeroes\n\nBecause we move the points by the minimum value for x, y, z\nrespectively, at least three beads will lie exactly on those three\nplanes. That suggests that at least one and at most 9 voxels that\nneighbor that bead in the negative domains in those spatial dimensions\nshould be filled in as well. But the voxel map only has a positive\ndomain.\n\nBefore, these voxels were not filled in.\n\nNow, we adjust the `min` Vec3 by subtracting one bead radius, moving the\nbeads exactly out of the way of that problem described above.","shortMessageHtmlLink":"voxelization: Fix three beads at axactly the axis-zeroes"}},{"before":"64f06772e3eace50a8b9410cee211f4825abbe09","after":"1bccc294cab557068d184ac27c4396ac9fcfd615","ref":"refs/heads/main","pushedAt":"2024-06-12T11:14:53.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Ensure at most the set number of rotations are placed\n\nBefore, it would be possible for more rotations to be tried than\nconfigured. This is unpredictable and the behavior tends to be dependent\non how dense the system is: low-density systems would be more likely to\nrespect the provided number of rotations than high-density systems,\nsince more attempts would be made with a new rotation set for each one.","shortMessageHtmlLink":"Ensure at most the set number of rotations are placed"}},{"before":"6a1aff1768c0fb862e9b7a1a5231bb67e47561e1","after":"64f06772e3eace50a8b9410cee211f4825abbe09","ref":"refs/heads/main","pushedAt":"2024-06-11T09:48:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Cache segment voxelizations\n\nThis prevents the voxelization for some rotation being determined for\nevery time `Segment.voxels()` is called. Now the voxelization is cached\nand this cache is invalidated when `Segment.set_rotation()` is called.","shortMessageHtmlLink":"Cache segment voxelizations"}},{"before":"81281192483b44e95bc9febb704f75c498b34a1f","after":"6a1aff1768c0fb862e9b7a1a5231bb67e47561e1","ref":"refs/heads/main","pushedAt":"2024-06-11T08:57:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Move bindings to render_placements to extensions","shortMessageHtmlLink":"Move bindings to render_placements to extensions"}},{"before":"2f79e959d034cc5886927f9330868b381d0f54e0","after":"4673fca3bf970a572a1ccb286134f7968099761b","ref":"refs/heads/26-compartment-defaults","pushedAt":"2024-05-30T09:51:02.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Update README to mention the implied default compartment\n\nDescribes the change proposed in #26.","shortMessageHtmlLink":"Update README to mention the implied default compartment"}},{"before":"9da52e3ac0f48c546b1ef4d085c82d1b959a7c0a","after":"2f79e959d034cc5886927f9330868b381d0f54e0","ref":"refs/heads/26-compartment-defaults","pushedAt":"2024-05-30T09:39:42.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Update README to mention the implied default compartment\n\nDescribes the change proposed in #26.","shortMessageHtmlLink":"Update README to mention the implied default compartment"}},{"before":"81281192483b44e95bc9febb704f75c498b34a1f","after":"9da52e3ac0f48c546b1ef4d085c82d1b959a7c0a","ref":"refs/heads/26-compartment-defaults","pushedAt":"2024-05-30T09:36:02.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Update README to mention the implied default compartment\n\nDescribes the change proposed in #26.","shortMessageHtmlLink":"Update README to mention the implied default compartment"}},{"before":null,"after":"81281192483b44e95bc9febb704f75c498b34a1f","ref":"refs/heads/26-compartment-defaults","pushedAt":"2024-05-30T08:46:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"check: Clarify that any structure file can be used as input\n\nSince we just use MDAnalysis to read in the structure, many structure\nfiles are supported, not just gro files.","shortMessageHtmlLink":"check: Clarify that any structure file can be used as input"}},{"before":"80ee643b958872adbf987c8d4f6f43b493c7a241","after":"81281192483b44e95bc9febb704f75c498b34a1f","ref":"refs/heads/main","pushedAt":"2024-05-23T10:52:53.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"check: Clarify that any structure file can be used as input\n\nSince we just use MDAnalysis to read in the structure, many structure\nfiles are supported, not just gro files.","shortMessageHtmlLink":"check: Clarify that any structure file can be used as input"}},{"before":"7a1295ec8085a1887ca00940f5504ef521dc1247","after":"80ee643b958872adbf987c8d4f6f43b493c7a241","ref":"refs/heads/main","pushedAt":"2024-05-18T13:57:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"pack: Fix abberant adjustment of placement list positions","shortMessageHtmlLink":"pack: Fix abberant adjustment of placement list positions"}},{"before":"dc444cb90e597270df8527c16b828099f75d2e62","after":"acca461ac0c7166ca76efd13cad994ffd4744e7c","ref":"refs/heads/check-command","pushedAt":"2024-05-16T16:01:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"check: Clarify that any structure file can be used as input\n\nSince we just use MDAnalysis to read in the structure, many structure\nfiles are supported, not just gro files.","shortMessageHtmlLink":"check: Clarify that any structure file can be used as input"}},{"before":"0106642cef35503a211ca5b52aacd52086e688d3","after":"dc444cb90e597270df8527c16b828099f75d2e62","ref":"refs/heads/check-command","pushedAt":"2024-05-16T15:55:57.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Add check subcommand\n\nThis subcommand will serve as a convenient way to check for collisions\nin generated structure files. Hopefully there are no such problems, but\nwith this tool, we can verify and find them more easily.","shortMessageHtmlLink":"Add check subcommand"}},{"before":null,"after":"0106642cef35503a211ca5b52aacd52086e688d3","ref":"refs/heads/check-command","pushedAt":"2024-05-16T15:54:16.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Add check subcommand\n\nThis subcommand will serve as a convenient way to check for collisions\nin generated structure files. Hopefully there are no such problems, but\nwith this tool, we can verify and find them more easily.","shortMessageHtmlLink":"Add check subcommand"}},{"before":"4b84ee19880d36f3e556a3932eb2939c10173677","after":"7a1295ec8085a1887ca00940f5504ef521dc1247","ref":"refs/heads/main","pushedAt":"2024-05-16T15:52:17.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"render: Introduce --resnum-mode option\n\nNow, bentopy render will write unique resnum for each placed instance by\ndefault.\n\nThe render-placements dependency was updated to version 0.2.1.","shortMessageHtmlLink":"render: Introduce --resnum-mode option"}},{"before":"1dcb7c5c29f81262c128a3d8723849f38c07bd64","after":"4b84ee19880d36f3e556a3932eb2939c10173677","ref":"refs/heads/main","pushedAt":"2024-05-16T14:32:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"render: Introduce --resnum-mode option\n\nNow, bentopy render will write unique resnum for each placed instance by\ndefault.\n\nThe render-placements dependency was updated to version 0.2.1.","shortMessageHtmlLink":"render: Introduce --resnum-mode option"}},{"before":"ba7aa1555803b862a5b4787d171dc96ec93f117b","after":"1dcb7c5c29f81262c128a3d8723849f38c07bd64","ref":"refs/heads/main","pushedAt":"2024-05-16T09:39:12.000Z","pushType":"pr_merge","commitsCount":7,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Document compartment constraint, rotation_axes, and center parameters\n\nBoth are hidden behind details blocks, since it's quite the flood of\ninformation for rather niche features.\n\nIssue #24 is mentioned in reference to the proposed `keep` value for\ncenter.","shortMessageHtmlLink":"Document compartment constraint, rotation_axes, and center parameters"}},{"before":"40196e63535ee5f4b2f5fab4127e072041404ad9","after":"ec3baedb856583a1622f7faf1d7ac0c4c72702e3","ref":"refs/heads/constraints","pushedAt":"2024-05-16T09:37:51.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"ma3ke","name":"Marieke Westendorp","path":"/ma3ke","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/17786929?s=80&v=4"},"commit":{"message":"Document compartment constraint, rotation_axes, and center parameters\n\nBoth are hidden behind details blocks, since it's quite the flood of\ninformation for rather niche features.\n\nIssue #24 is mentioned in reference to the proposed `keep` value for\ncenter.","shortMessageHtmlLink":"Document compartment constraint, rotation_axes, and center parameters"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEbo_JIAA","startCursor":null,"endCursor":null}},"title":"Activity · marrink-lab/bentopy"}