{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":142321950,"defaultBranch":"main","name":"pyPESTO","ownerLogin":"ICB-DCM","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-07-25T15:51:29.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/17879961?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726844329.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"567815014300c39dca431f2775ae7eab776098a0","ref":"refs/heads/fix_1461_test_bridge_sampling","pushedAt":"2024-09-20T14:58:49.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"arrjon","name":"Jonas Arruda","path":"/arrjon","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69197639?s=80&v=4"},"commit":{"message":"change test_bridge_sampling to laplace","shortMessageHtmlLink":"change test_bridge_sampling to laplace"}},{"before":"cbf26b8ac90ea89a4e4df2278fcd3523bfbb5154","after":"ad8e004e5eea5ed4a3830e44cef522d7c4ba3144","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-20T12:49:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"changed julia notebooks ever so slightly.","shortMessageHtmlLink":"changed julia notebooks ever so slightly."}},{"before":null,"after":"dd8f877a277ec6b4aacb5e31074694f7f742d53c","ref":"refs/heads/fixed_gap_ordinal","pushedAt":"2024-09-19T12:46:04.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"Doresic","name":null,"path":"/Doresic","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85789271?s=80&v=4"},"commit":{"message":"Fix the gap and interval constraints to some values","shortMessageHtmlLink":"Fix the gap and interval constraints to some values"}},{"before":null,"after":"dfb33ace8aace3bc24ab14c1a902a75258873579","ref":"refs/heads/more_informative_info","pushedAt":"2024-09-19T11:00:09.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"More informative info message for start indices.","shortMessageHtmlLink":"More informative info message for start indices."}},{"before":"0e9d274eec7cb774024427872f21da4833497670","after":"cbf26b8ac90ea89a4e4df2278fcd3523bfbb5154","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-19T10:59:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"for now: more starts with pyswarms.","shortMessageHtmlLink":"for now: more starts with pyswarms."}},{"before":"b6c16245830ec315e09c5bd59e82c832720dac82","after":"0e9d274eec7cb774024427872f21da4833497670","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-19T09:20:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"fixed custom_objective_function","shortMessageHtmlLink":"fixed custom_objective_function"}},{"before":"bfac160ade2f7a129a0b652e469fa07e7dd185fc","after":"b6c16245830ec315e09c5bd59e82c832720dac82","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-19T08:28:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Start out with boehm, for optimization etc change to conversion reaction","shortMessageHtmlLink":"Start out with boehm, for optimization etc change to conversion reaction"}},{"before":"646b7fe389e4f5637990f20a61fcb4c0956e095a","after":"bfac160ade2f7a129a0b652e469fa07e7dd185fc","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-19T07:40:46.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"changed directory II","shortMessageHtmlLink":"changed directory II"}},{"before":"a1a54f771815ba2579259082dff59e045188dd12","after":"646b7fe389e4f5637990f20a61fcb4c0956e095a","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-19T07:13:44.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"reverted changes and kept original structure. adjusted amici.ipynb","shortMessageHtmlLink":"reverted changes and kept original structure. adjusted amici.ipynb"}},{"before":"7fb1b5acd378de164f9f82de8c4ca637e15aaddd","after":"a1a54f771815ba2579259082dff59e045188dd12","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-18T10:43:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"renamed \"model_conversion_reaction\" to \"conversion_reaction\" according to naming scheme in benchmark models as well","shortMessageHtmlLink":"renamed \"model_conversion_reaction\" to \"conversion_reaction\" accordin…"}},{"before":"aa88768fd7b797cdf65990014594d63e1c4a9790","after":"7fb1b5acd378de164f9f82de8c4ca637e15aaddd","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-18T09:31:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Correctly install pyswarms in notebooks1","shortMessageHtmlLink":"Correctly install pyswarms in notebooks1"}},{"before":null,"after":"aa88768fd7b797cdf65990014594d63e1c4a9790","ref":"refs/heads/brush_over_notebooks","pushedAt":"2024-09-18T09:24:47.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"shortening many optimizations. Replacing Boehm with conversion reaction where possible. Thermodynamic more robust.","shortMessageHtmlLink":"shortening many optimizations. Replacing Boehm with conversion reacti…"}},{"before":"c404fa6ca12b95d5f135ecb920463b08baf7f4f6","after":"0cc72e96f6b8a92b277fdebe5df05aa225d04005","ref":"refs/heads/prepare_release_0.5.4","pushedAt":"2024-09-17T14:41:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Fixed typo","shortMessageHtmlLink":"Fixed typo"}},{"before":null,"after":"c404fa6ca12b95d5f135ecb920463b08baf7f4f6","ref":"refs/heads/prepare_release_0.5.4","pushedAt":"2024-09-17T14:40:10.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Updated changelog and readthedocs","shortMessageHtmlLink":"Updated changelog and readthedocs"}},{"before":"a09e8bf4b0e3cf99017d6f7cc43e7368ae56902e","after":"983da42b7ffb02ca90506a64789b9a83ed5a5ef6","ref":"refs/heads/petab_simulator_support","pushedAt":"2024-09-17T14:15:28.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Merge branch 'develop' into petab_simulator_support","shortMessageHtmlLink":"Merge branch 'develop' into petab_simulator_support"}},{"before":"b88356f3666af8908e7796ea6fae6856bbc77319","after":"881b4dc0848d88f12ffa95c7eba016d5ea8f4257","ref":"refs/heads/fix_semiquant_solver","pushedAt":"2024-09-17T13:29:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"Doresic","name":null,"path":"/Doresic","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85789271?s=80&v=4"},"commit":{"message":"TODO still need to remove a lot of commented out stuff","shortMessageHtmlLink":"TODO still need to remove a lot of commented out stuff"}},{"before":null,"after":"b88356f3666af8908e7796ea6fae6856bbc77319","ref":"refs/heads/fix_semiquant_solver","pushedAt":"2024-09-17T13:28:35.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"Doresic","name":null,"path":"/Doresic","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/85789271?s=80&v=4"},"commit":{"message":"SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximity check (#1462)\n\nPreviously, the distance was scaled to the second point, which didn't make too much sense.\r\nNow it's scaled to the parameter bounds.","shortMessageHtmlLink":"SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximi…"}},{"before":"5c58374fa966b0669b4270e952e066220f158959","after":"b88356f3666af8908e7796ea6fae6856bbc77319","ref":"refs/heads/develop","pushedAt":"2024-09-16T14:27:13.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"dweindl","name":"Daniel Weindl","path":"/dweindl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048784?s=80&v=4"},"commit":{"message":"SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximity check (#1462)\n\nPreviously, the distance was scaled to the second point, which didn't make too much sense.\r\nNow it's scaled to the parameter bounds.","shortMessageHtmlLink":"SacessOptimizer, ESSOptimizer: Bound-normalize parameters for proximi…"}},{"before":null,"after":"5acf73aa80f2e56c1e0a2fc01f21db84313c2849","ref":"refs/heads/fix_1463","pushedAt":"2024-09-16T14:10:29.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"FFroehlich","name":"Fabian Fröhlich","path":"/FFroehlich","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/14923969?s=80&v=4"},"commit":{"message":"attempt fix + add test","shortMessageHtmlLink":"attempt fix + add test"}},{"before":"36eec04a09f0a1e0a34d6db097141756ef9096df","after":"5c58374fa966b0669b4270e952e066220f158959","ref":"refs/heads/develop","pushedAt":"2024-09-16T12:02:14.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"dweindl","name":"Daniel Weindl","path":"/dweindl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048784?s=80&v=4"},"commit":{"message":"SacessOptimizer: expose more hyperparameters + minor fixes (#1459)\n\n* Introduces a new SacessOptions class to collect SacessOptimizer hyperparameters and makes some previously hard-coded values configurable.\r\n\r\n  Closes #1458\r\n\r\n* Fixes a mismatch in adaptation conditions between the original SaCeSS implementation and SacessOptimizer (adaptation condition: AND -> OR)\r\n\r\n* Log final worker configuration\r\n\r\n* Sort refset before resizing.","shortMessageHtmlLink":"SacessOptimizer: expose more hyperparameters + minor fixes (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2526501375\" data-permission-text=\"Title is private\" data-url=\"https://github.com/ICB-DCM/pyPESTO/issues/1459\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/ICB-DCM/pyPESTO/pull/1459/hovercard\" href=\"https://github.com/ICB-DCM/pyPESTO/pull/1459\">#1459</a>)"}},{"before":"fde7b07d691c73ef3385717ef84f271b35a549d4","after":"a09e8bf4b0e3cf99017d6f7cc43e7368ae56902e","ref":"refs/heads/petab_simulator_support","pushedAt":"2024-09-16T09:50:33.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Merge branch 'develop' into petab_simulator_support","shortMessageHtmlLink":"Merge branch 'develop' into petab_simulator_support"}},{"before":"20057d5c475d9927e1c55a90ad67c1d4acfcd25d","after":"fde7b07d691c73ef3385717ef84f271b35a549d4","ref":"refs/heads/petab_simulator_support","pushedAt":"2024-09-16T09:31:04.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"added option to pass simulator type and simulator to create_objective_creator","shortMessageHtmlLink":"added option to pass simulator type and simulator to create_objective…"}},{"before":"2831e47a12de6bcab4a964babacff644d8ae3f5d","after":"20057d5c475d9927e1c55a90ad67c1d4acfcd25d","ref":"refs/heads/petab_simulator_support","pushedAt":"2024-09-16T08:50:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Update doc/example/petab_import.ipynb\n\nCo-authored-by: Fabian Fröhlich <fabian.frohlich@crick.ac.uk>","shortMessageHtmlLink":"Update doc/example/petab_import.ipynb"}},{"before":"f65928d2b022879670e8b1b9d28c9c3666f09096","after":"36eec04a09f0a1e0a34d6db097141756ef9096df","ref":"refs/heads/develop","pushedAt":"2024-09-15T07:58:17.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"dweindl","name":"Daniel Weindl","path":"/dweindl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048784?s=80&v=4"},"commit":{"message":"SacessOptimizer: Fix acceptance threshold for objective improvement (#1457)\n\nThere seems to be a difference in the acceptance threshold for objective improvement that is reported in the sacess paper and the value that is used in the implementation. Changing to the value used in the original implementation.\r\n\r\nFor the manager:\r\n[Paper](https://doi.org/10.1186/s12859-016-1452-4): 10%\r\nImplementation accompanying the paper: [0.5%](https://bitbucket.org/DavidPenas/sacess-library/src/18b2027af5b97158e5d5303487455e5e529bcf5a/src/method_module_fortran/eSS/parallelscattersearchfunctions.f90#lines-388) \r\nMore [recent](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011151) implementation: [0.01%](https://bitbucket.org/DavidPenas/sacess-library/src/508e7ac15579104731cf1f8c3969960c6e72b872/src/method_module_fortran/eSS/parallelscattersearchfunctions.f90#lines-396)\r\nAlso added a check for the minimum acceptance threshold as in the original implementation. \r\n\r\nFor the workers: \r\nshould be 0.01% instead 0.01.","shortMessageHtmlLink":"SacessOptimizer: Fix acceptance threshold for objective improvement (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2524568147\" data-permission-text=\"Title is private\" data-url=\"https://github.com/ICB-DCM/pyPESTO/issues/1457\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/ICB-DCM/pyPESTO/pull/1457/hovercard\" href=\"https://github.com/ICB-DCM/pyPESTO/pull/1457\">#…</a>"}},{"before":"fd652e80f72ba83246ecd70980be22b4a6c5fad1","after":"f65928d2b022879670e8b1b9d28c9c3666f09096","ref":"refs/heads/develop","pushedAt":"2024-09-13T09:45:46.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"dweindl","name":"Daniel Weindl","path":"/dweindl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048784?s=80&v=4"},"commit":{"message":"Doc: fix formatting (#1456)\n\nFix list formatting in doc/example/model_evidence_and_bayes_factors.ipynb,\r\nget rid of ipywidgets warning, and fix typo.","shortMessageHtmlLink":"Doc: fix formatting (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2523955419\" data-permission-text=\"Title is private\" data-url=\"https://github.com/ICB-DCM/pyPESTO/issues/1456\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/ICB-DCM/pyPESTO/pull/1456/hovercard\" href=\"https://github.com/ICB-DCM/pyPESTO/pull/1456\">#1456</a>)"}},{"before":"0d549c20946fac0b7abac337861ed19110d5d7b6","after":null,"ref":"refs/heads/bayes_factor_tutorial","pushedAt":"2024-09-12T10:38:26.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"arrjon","name":"Jonas Arruda","path":"/arrjon","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69197639?s=80&v=4"}},{"before":"0465922f320abc4c10d14173a8e440a37505c345","after":"fd652e80f72ba83246ecd70980be22b4a6c5fad1","ref":"refs/heads/develop","pushedAt":"2024-09-12T10:38:08.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"arrjon","name":"Jonas Arruda","path":"/arrjon","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/69197639?s=80&v=4"},"commit":{"message":"Bayes factor Tutorial (#1444)\n\n* adding utilities to compute Bayes Factor\r\n\r\n* adding tutorial on Bayes Factors","shortMessageHtmlLink":"Bayes factor Tutorial (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2453576226\" data-permission-text=\"Title is private\" data-url=\"https://github.com/ICB-DCM/pyPESTO/issues/1444\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/ICB-DCM/pyPESTO/pull/1444/hovercard\" href=\"https://github.com/ICB-DCM/pyPESTO/pull/1444\">#1444</a>)"}},{"before":"5e5be6dc28d4327034a28665e986e7df7999e8bf","after":"2831e47a12de6bcab4a964babacff644d8ae3f5d","ref":"refs/heads/petab_simulator_support","pushedAt":"2024-09-11T12:08:41.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Merge branch 'develop' into petab_simulator_support","shortMessageHtmlLink":"Merge branch 'develop' into petab_simulator_support"}},{"before":"7d528c0e1fb3a072bfe1ea1d98f6c8e7b4fb15eb","after":"0d549c20946fac0b7abac337861ed19110d5d7b6","ref":"refs/heads/bayes_factor_tutorial","pushedAt":"2024-09-11T12:07:28.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"},"commit":{"message":"Merge branch 'develop' into bayes_factor_tutorial","shortMessageHtmlLink":"Merge branch 'develop' into bayes_factor_tutorial"}},{"before":"808e21069941c288e8afce66ae0e0ce288b4ef64","after":null,"ref":"refs/heads/remove_aesara","pushedAt":"2024-09-11T12:06:50.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"PaulJonasJost","name":"Paul Jonas Jost","path":"/PaulJonasJost","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/70631928?s=80&v=4"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMFQxNDo1ODo0OS4wMDAwMDBazwAAAAS8FsVz","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMFQxNDo1ODo0OS4wMDAwMDBazwAAAAS8FsVz","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xMVQxMjowNjo1MC4wMDAwMDBazwAAAASzJree"}},"title":"Activity · ICB-DCM/pyPESTO"}