{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":209079824,"defaultBranch":"master","name":"oxDNA","ownerLogin":"lorenzo-rovigatti","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2019-09-17T14:41:57.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/68116?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1715019923.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"b904dea92f883cafa7de49ef5693996fc4ffc99f","ref":"refs/heads/dependabot/pip/docs/jinja2-3.1.4","pushedAt":"2024-05-06T18:25:23.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dependabot[bot]","name":null,"path":"/apps/dependabot","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/29110?s=80&v=4"},"commit":{"message":"Bump jinja2 from 3.0.3 to 3.1.4 in /docs\n\nBumps [jinja2](https://github.com/pallets/jinja) from 3.0.3 to 3.1.4.\n- [Release notes](https://github.com/pallets/jinja/releases)\n- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)\n- [Commits](https://github.com/pallets/jinja/compare/3.0.3...3.1.4)\n\n---\nupdated-dependencies:\n- dependency-name: jinja2\n dependency-type: direct:production\n...\n\nSigned-off-by: dependabot[bot] ","shortMessageHtmlLink":"Bump jinja2 from 3.0.3 to 3.1.4 in /docs"}},{"before":"e882b42c132aaef1210d8966c8ff1f8680afbfd1","after":"dbdc72658ff0325910c50586e16427c45a767f44","ref":"refs/heads/master","pushedAt":"2024-04-16T14:30:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Add an optional Yukawa repulsion to the CPU DPS model","shortMessageHtmlLink":"Add an optional Yukawa repulsion to the CPU DPS model"}},{"before":"2b93f63a751f6af9d37b945ff9c2c383512d67d2","after":"e882b42c132aaef1210d8966c8ff1f8680afbfd1","ref":"refs/heads/master","pushedAt":"2024-04-06T14:31:01.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA"}},{"before":"2d33bcc29715de82adad39be076ec5045d32e671","after":"2b93f63a751f6af9d37b945ff9c2c383512d67d2","ref":"refs/heads/master","pushedAt":"2024-03-28T22:16:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix #97\n\nThe commit fixes a couple of issues linked to static variables, and also makes the code throw an exception if an OxpyManager is initialised without first destroying previous instances.","shortMessageHtmlLink":"Fix #97"}},{"before":"9af1214a7ddaa5f9aeac8220476ce5b9e0aed9b6","after":"2d33bcc29715de82adad39be076ec5045d32e671","ref":"refs/heads/master","pushedAt":"2024-03-25T10:12:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"DPS: Fix a bug whereby species with 0 particles would not be handled correctly","shortMessageHtmlLink":"DPS: Fix a bug whereby species with 0 particles would not be handled …"}},{"before":"610df730c5f96128b456c99e58d296a3cd60561d","after":"1f2d3cc8ea43ded7b4a72da67a70ba003d5c6ef7","ref":"refs/heads/gh-pages","pushedAt":"2024-03-22T15:57:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Update documentation","shortMessageHtmlLink":"Update documentation"}},{"before":"35682563d2068295c8d1fc77cc12299772dcb21e","after":"9af1214a7ddaa5f9aeac8220476ce5b9e0aed9b6","ref":"refs/heads/master","pushedAt":"2024-03-22T15:54:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix the documentations for the structure factor observable","shortMessageHtmlLink":"Fix the documentations for the structure factor observable"}},{"before":"bc2de60be9f82adf9cb371bc0749364ef8300991","after":"35682563d2068295c8d1fc77cc12299772dcb21e","ref":"refs/heads/master","pushedAt":"2024-03-18T16:39:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Port the ANNaMo interaction to CUDA","shortMessageHtmlLink":"Port the ANNaMo interaction to CUDA"}},{"before":"83e30d79a5592a3b9e7d7227e00c366e00ba3150","after":"bc2de60be9f82adf9cb371bc0749364ef8300991","ref":"refs/heads/master","pushedAt":"2024-03-18T13:46:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Update errors and docstrings in duplex_angle_plotter","shortMessageHtmlLink":"Update errors and docstrings in duplex_angle_plotter"}},{"before":"2638bd390e53c3cf04271d984563d7fe7d2990f5","after":"610df730c5f96128b456c99e58d296a3cd60561d","ref":"refs/heads/gh-pages","pushedAt":"2024-03-18T13:20:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Update documentation","shortMessageHtmlLink":"Update documentation"}},{"before":"eb17a42f089961f37c05b0b187c59f9a6f143f1a","after":"83e30d79a5592a3b9e7d7227e00c366e00ba3150","ref":"refs/heads/master","pushedAt":"2024-03-18T13:17:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Fixed type hint that was breaking the docs","shortMessageHtmlLink":"Fixed type hint that was breaking the docs"}},{"before":"51f11d4748429dadf83c3f51a94009a3a74211b6","after":"eb17a42f089961f37c05b0b187c59f9a6f143f1a","ref":"refs/heads/master","pushedAt":"2024-03-18T13:09:23.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Duplex angle plotter now works with ANY nucleotide id in the duplex, not just start/end. Bumped version number.","shortMessageHtmlLink":"Duplex angle plotter now works with ANY nucleotide id in the duplex, …"}},{"before":"07e38cf09830f2078ccf993b122848fdcecbc7d9","after":"51f11d4748429dadf83c3f51a94009a3a74211b6","ref":"refs/heads/master","pushedAt":"2024-03-15T20:57:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Added quiet flag to all oat scripts to silence INFO prints. Settings for logging are in UTILS.logger.logger_settings","shortMessageHtmlLink":"Added quiet flag to all oat scripts to silence INFO prints. Settings …"}},{"before":"601e3ce85f3108330e15facb8763339b7c8f64f0","after":"07e38cf09830f2078ccf993b122848fdcecbc7d9","ref":"refs/heads/master","pushedAt":"2024-03-15T16:18:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Make the CUDA NA interaction runnable","shortMessageHtmlLink":"Make the CUDA NA interaction runnable"}},{"before":"6854eece35de6723abe81e6e64d598ef12c5a302","after":"601e3ce85f3108330e15facb8763339b7c8f64f0","ref":"refs/heads/master","pushedAt":"2024-03-14T16:12:57.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix rcut for unbonded pairs (#93)","shortMessageHtmlLink":"Fix rcut for unbonded pairs (#93)"}},{"before":"97290e3a5ac0da317d2f7c1fab040507106dafa8","after":"2638bd390e53c3cf04271d984563d7fe7d2990f5","ref":"refs/heads/gh-pages","pushedAt":"2024-03-12T12:21:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Update documentation","shortMessageHtmlLink":"Update documentation"}},{"before":"80920abbefc93271ea6b244dea8aabf6334e1b9d","after":"6854eece35de6723abe81e6e64d598ef12c5a302","ref":"refs/heads/master","pushedAt":"2024-03-12T12:15:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Update the CHANGELOG to prepare for the new version","shortMessageHtmlLink":"Update the CHANGELOG to prepare for the new version"}},{"before":"51de178648bac64e0ad87ff33b59eb3a013ee12e","after":"80920abbefc93271ea6b244dea8aabf6334e1b9d","ref":"refs/heads/master","pushedAt":"2024-03-07T17:11:43.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"overhaul of clustering to have significantly more options and cleaner output","shortMessageHtmlLink":"overhaul of clustering to have significantly more options and cleaner…"}},{"before":"0e5c28d821d0ae3a3c6b80e496df5ce5aa88c290","after":"51de178648bac64e0ad87ff33b59eb3a013ee12e","ref":"refs/heads/master","pushedAt":"2024-03-06T14:31:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"bump oat version number -- documentation updates and bugfixes to file I/O in mulitple scripts","shortMessageHtmlLink":"bump oat version number -- documentation updates and bugfixes to file…"}},{"before":"3d316b649d2406d33b19efa55446dc3ce99a68e8","after":"0e5c28d821d0ae3a3c6b80e496df5ce5aa88c290","ref":"refs/heads/master","pushedAt":"2024-03-06T14:16:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"fixed missing newline bug in write_conf","shortMessageHtmlLink":"fixed missing newline bug in write_conf"}},{"before":"f0da29b32f0c12388dfeff0f77b8ec8218b77346","after":"3d316b649d2406d33b19efa55446dc3ce99a68e8","ref":"refs/heads/master","pushedAt":"2024-03-05T17:09:53.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"added output file naming option to superimpose","shortMessageHtmlLink":"added output file naming option to superimpose"}},{"before":"47247149d824d99f47cb7a8cda0010947d952618","after":"f0da29b32f0c12388dfeff0f77b8ec8218b77346","ref":"refs/heads/master","pushedAt":"2024-03-04T13:31:56.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA"}},{"before":"c3caa198822a9b6ee4246ae749f733a4a15ecdd0","after":"47247149d824d99f47cb7a8cda0010947d952618","ref":"refs/heads/master","pushedAt":"2024-03-01T20:38:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix a bug whereby unnormalised patches were not working correctly with CUDA","shortMessageHtmlLink":"Fix a bug whereby unnormalised patches were not working correctly wit…"}},{"before":"29a57f4c9208da89a2d325d2eada2f590795e2ab","after":"c3caa198822a9b6ee4246ae749f733a4a15ecdd0","ref":"refs/heads/master","pushedAt":"2024-03-01T20:32:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Make it possible to use unnormalised patches with the DPS interaction","shortMessageHtmlLink":"Make it possible to use unnormalised patches with the DPS interaction"}},{"before":"4978ae1a9f216b95d97e5703a22ec1888112c998","after":"29a57f4c9208da89a2d325d2eada2f590795e2ab","ref":"refs/heads/master","pushedAt":"2024-03-01T15:10:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix a bug whereby the DPS interaction would give different results on CPU and GPU when used with custom patches","shortMessageHtmlLink":"Fix a bug whereby the DPS interaction would give different results on…"}},{"before":"a43193c9dd9b7b4be9bca52832e6d1d3af76553c","after":"4978ae1a9f216b95d97e5703a22ec1888112c998","ref":"refs/heads/master","pushedAt":"2024-02-23T10:15:09.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ErikPoppleton","name":"Erik Poppleton","path":"/ErikPoppleton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/36451772?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA"}},{"before":"b38ae1c658bde7c4edd4769a89532f65df877894","after":"a43193c9dd9b7b4be9bca52832e6d1d3af76553c","ref":"refs/heads/master","pushedAt":"2024-02-20T15:54:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"zoombya","name":"Michael Matthies","path":"/zoombya","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1756978?s=80&v=4"},"commit":{"message":"Update oat boilerplate.py \n\n- updated to the latest python\r\n- fixed trajectory view\r\n- Simulation now runs in the simulation folder","shortMessageHtmlLink":"Update oat boilerplate.py"}},{"before":"f6970718199144ffe718c4a4e9652b16ce738e2e","after":"b38ae1c658bde7c4edd4769a89532f65df877894","ref":"refs/heads/master","pushedAt":"2024-02-18T20:44:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix a bug whereby the DPS interaction would segfault instead of exiting with an error when too many patches were used","shortMessageHtmlLink":"Fix a bug whereby the DPS interaction would segfault instead of exiti…"}},{"before":"7f0eff61298a208eb31f1258631e974ee34ed529","after":"f6970718199144ffe718c4a4e9652b16ce738e2e","ref":"refs/heads/master","pushedAt":"2024-02-08T14:09:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Fix a bug whereby an output would be opened even when initialised with only_last = true","shortMessageHtmlLink":"Fix a bug whereby an output would be opened even when initialised wit…"}},{"before":"5404bb08a3d4c070abe6b80a1746dc20d6c15172","after":"7f0eff61298a208eb31f1258631e974ee34ed529","ref":"refs/heads/master","pushedAt":"2024-02-04T22:32:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lorenzo-rovigatti","name":"Lorenzo Rovigatti","path":"/lorenzo-rovigatti","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68116?s=80&v=4"},"commit":{"message":"Make the `external_force` observable work","shortMessageHtmlLink":"Make the external_force observable work"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEQtHPNAA","startCursor":null,"endCursor":null}},"title":"Activity · lorenzo-rovigatti/oxDNA"}