{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":439429945,"defaultBranch":"main","name":"ExampleNotebooks","ownerLogin":"OpenFreeEnergy","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-12-17T18:44:46.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/92118939?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1714666735.0","currentOid":""},"activityList":{"items":[{"before":"9fea50f196363212f47be84eea60d80e17114b3a","after":null,"ref":"refs/tags/april-2024","pushedAt":"2024-05-02T16:18:31.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"}},{"before":"9fea50f196363212f47be84eea60d80e17114b3a","after":null,"ref":"refs/tags/may-2023","pushedAt":"2024-05-02T16:18:25.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"}},{"before":"b70d4329a8ac8c29a22a84b35c3194bff524c605","after":"41b8bf740900bab79c80b08691d02f443081d50a","ref":"refs/heads/main","pushedAt":"2024-05-02T16:17:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"update links in readme","shortMessageHtmlLink":"update links in readme"}},{"before":"bd4958f5ef080c7b12d7769d0e0252fa1d159469","after":null,"ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T16:13:14.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"}},{"before":"9fea50f196363212f47be84eea60d80e17114b3a","after":"b70d4329a8ac8c29a22a84b35c3194bff524c605","ref":"refs/heads/main","pushedAt":"2024-05-02T16:13:13.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"Test openfe 1.0.0rc0 + refresh showcase (#99)\n\n* spruce up CI\r\n\r\n* now test the rc\r\n\r\n* Fix choose_protocol.ipynb\r\n\r\n* Duplicate openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb history in showcase/openfe_showcase.ipynb history.\r\n\r\n* shave and a haircut - 2 bits\r\n\r\n* Fix showcase tutorial (#101)\r\n\r\n* fix showcase notebook\r\n\r\n* small fixes\r\n\r\n* added some stuff from hannah pr\r\n\r\n* update ligand_networks_for_developers.ipynb for 1.0rc0\r\n\r\n* update benchmark_demo.ipynb for 1.0rc0\r\n\r\n* first stab at changing examples to tyk2\r\n\r\n* more switches to tyk2\r\n\r\n* Add TYK2 image, remove T4L references\r\n\r\n* Remove output\r\n\r\n* Remove atom mapping CLI stuff\r\n\r\n* show options atom mappers and ligand networks\r\n\r\n* more notebook changes\r\n\r\n* Add tyk2 figure and logo\r\n\r\n* more changes showcase notebook\r\n\r\n* Adress review comments\r\n\r\n* Addressing review comments\r\n\r\n* fix mapping\r\n\r\n* transformation inputs as bullet points\r\n\r\n* see if python 3.10 works\r\n\r\n* lets see which python versions will work\r\n\r\n* rerun ci\r\n\r\n* update url for showcase installer\r\n\r\n* unpin python version in env\r\n\r\n* remove cell merged in by mistake\r\n\r\n* see issue https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138\r\n\r\n* some small fixes for google colab\r\n\r\n* just test on python 3.10\r\n\r\n* pull down inputs for showcase\r\n\r\n* drop osx for now\r\n\r\n* put inputs in correct location\r\n\r\n* updated with results, see issue https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/141\r\n\r\n* skip running nbval on openfe gather cells at the end\r\n\r\n* fix url for download\r\n\r\n* update manual spec of default settings for openff bump\r\n\r\nthis is now 2.1.1 in 1.0 of openfe\r\n\r\n* use fetch results for demoing gather\r\n\r\n* use fetch to pull in inputs\r\n\r\n* we can run more cells in CI, also added a note about it being a single edige\r\n\r\n* fix Analysis typo\r\n\r\n* pulled down wrong inputs\r\n\r\n* Added a hack for google colab\r\n\r\n---------\r\n\r\nCo-authored-by: hannahbaumann \r\nCo-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>\r\nCo-authored-by: richard gowers \r\nCo-authored-by: Irfan Alibay ","shortMessageHtmlLink":"Test openfe 1.0.0rc0 + refresh showcase (#99)"}},{"before":"630e5fa75abc6a8d3662ce07e3e3fc25b8dc0434","after":"bd4958f5ef080c7b12d7769d0e0252fa1d159469","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T16:12:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"comment out assert","shortMessageHtmlLink":"comment out assert"}},{"before":"8349468e04e9967c69ab6d4965a1509e14ae44f1","after":"630e5fa75abc6a8d3662ce07e3e3fc25b8dc0434","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T15:38:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"Added a hack for google colab","shortMessageHtmlLink":"Added a hack for google colab"}},{"before":"33cca55675bd0b56482a61816eaf6679028745c3","after":"8349468e04e9967c69ab6d4965a1509e14ae44f1","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T14:43:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"pulled down wrong inputs","shortMessageHtmlLink":"pulled down wrong inputs"}},{"before":"9c04a1e1403a267b4371b61d95a61faa5be059c9","after":"33cca55675bd0b56482a61816eaf6679028745c3","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T14:18:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"fix Analysis typo","shortMessageHtmlLink":"fix Analysis typo"}},{"before":"034aabf6233dc15256a0b6a9a25d1c6b2c29bcf9","after":"9c04a1e1403a267b4371b61d95a61faa5be059c9","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T14:17:17.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"we can run more cells in CI, also added a note about it being a single edige","shortMessageHtmlLink":"we can run more cells in CI, also added a note about it being a singl…"}},{"before":"7143aca2f8b34cc1c90bb5869ba63a81fbfcb10c","after":"034aabf6233dc15256a0b6a9a25d1c6b2c29bcf9","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T14:02:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"richardjgowers","name":"Richard Gowers","path":"/richardjgowers","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9249543?s=80&v=4"},"commit":{"message":"use fetch results for demoing gather","shortMessageHtmlLink":"use fetch results for demoing gather"}},{"before":"2e2cf45a8df3b068e72c2efb2995787b7f9f4a50","after":"7143aca2f8b34cc1c90bb5869ba63a81fbfcb10c","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T12:18:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"richardjgowers","name":"Richard Gowers","path":"/richardjgowers","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9249543?s=80&v=4"},"commit":{"message":"update manual spec of default settings for openff bump\n\nthis is now 2.1.1 in 1.0 of openfe","shortMessageHtmlLink":"update manual spec of default settings for openff bump"}},{"before":"e479c6d9008e6c8f71be025d9a46a6c93cdd7b1c","after":"2e2cf45a8df3b068e72c2efb2995787b7f9f4a50","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T00:25:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"fix url for download","shortMessageHtmlLink":"fix url for download"}},{"before":"59e60606e6940796d2d8dbebb3c970877965ac8d","after":"e479c6d9008e6c8f71be025d9a46a6c93cdd7b1c","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T00:24:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"skip running nbval on openfe gather cells at the end","shortMessageHtmlLink":"skip running nbval on openfe gather cells at the end"}},{"before":"553d5141f7d420d1183a4f14d57337389a905468","after":"59e60606e6940796d2d8dbebb3c970877965ac8d","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-02T00:11:36.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"updated with results, see issue https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/141","shortMessageHtmlLink":"updated with results, see issue #141"}},{"before":"777d72b1c4fc2b22a9bd94fe3fe84ec7063f8f19","after":"553d5141f7d420d1183a4f14d57337389a905468","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T20:44:01.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"pull down inputs for showcase","shortMessageHtmlLink":"pull down inputs for showcase"}},{"before":"daa75381403a292a851bdfa965726d51700352fd","after":"777d72b1c4fc2b22a9bd94fe3fe84ec7063f8f19","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T19:57:56.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"see issue https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138","shortMessageHtmlLink":"see issue #138"}},{"before":"0db94add19b35ac43a78fdb46857a12af9253a2a","after":"daa75381403a292a851bdfa965726d51700352fd","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:57:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"unpin python version in env","shortMessageHtmlLink":"unpin python version in env"}},{"before":"7db67b4221bce94bfb5f9d926243f3815b7ceeb7","after":"0db94add19b35ac43a78fdb46857a12af9253a2a","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:45:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"update url for showcase installer","shortMessageHtmlLink":"update url for showcase installer"}},{"before":"f9e196819399dced98d57d2b6740fd247e34ea91","after":"7db67b4221bce94bfb5f9d926243f3815b7ceeb7","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:42:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"rerun ci","shortMessageHtmlLink":"rerun ci"}},{"before":"dffda7fc49a8c4323e3be5be5c0d113c2124b52c","after":"f9e196819399dced98d57d2b6740fd247e34ea91","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:30:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"lets see which python versions will work","shortMessageHtmlLink":"lets see which python versions will work"}},{"before":"edfd2eaef7e862c38dc0d3564ac8d08afd10597a","after":"dffda7fc49a8c4323e3be5be5c0d113c2124b52c","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:29:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"see if python 3.10 works","shortMessageHtmlLink":"see if python 3.10 works"}},{"before":"1ae7400aaefae8b196c153137c4712686ad24c3b","after":"edfd2eaef7e862c38dc0d3564ac8d08afd10597a","ref":"refs/heads/openfe-1.0.0rc0-test","pushedAt":"2024-05-01T18:24:30.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/main' into openfe-1.0.0rc0-test","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/main' into openfe-1.0.0rc0-test"}},{"before":"fb14d5863bd6a9299f7173dfa9abef9dead7b504","after":null,"ref":"refs/heads/pin-macos-runner-to-v12","pushedAt":"2024-04-30T15:04:47.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"}},{"before":"7a9611e767395b3cc143f08399e02bccc9cf7e37","after":"9fea50f196363212f47be84eea60d80e17114b3a","ref":"refs/heads/main","pushedAt":"2024-04-30T15:04:46.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"Pin macos runner to v12 (#134)\n\n* pin macos runner\r\n\r\n* add note","shortMessageHtmlLink":"Pin macos runner to v12 (#134)"}},{"before":"284f0fb813c32ad4d980f9769822abc1e45ac68d","after":null,"ref":"refs/heads/845-run-through-tutorial-using-10-release-1","pushedAt":"2024-04-30T10:24:13.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"IAlibay","name":"Irfan Alibay","path":"/IAlibay","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12460125?s=80&v=4"}},{"before":"de3a0819f1139f41482ae58029d6ae97a4d6dd9f","after":"7a9611e767395b3cc143f08399e02bccc9cf7e37","ref":"refs/heads/main","pushedAt":"2024-04-30T10:24:12.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"IAlibay","name":"Irfan Alibay","path":"/IAlibay","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/12460125?s=80&v=4"},"commit":{"message":"Merge pull request #137 from OpenFreeEnergy/845-run-through-tutorial-using-10-release-1\n\nPolish up the RBFE CLI tutorial for 1.0 release","shortMessageHtmlLink":"Merge pull request #137 from OpenFreeEnergy/845-run-through-tutorial-…"}},{"before":"de3a0819f1139f41482ae58029d6ae97a4d6dd9f","after":"284f0fb813c32ad4d980f9769822abc1e45ac68d","ref":"refs/heads/845-run-through-tutorial-using-10-release-1","pushedAt":"2024-04-29T19:57:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jameseastwood","name":"James R. Baggs Eastwood","path":"/jameseastwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1616602?s=80&v=4"},"commit":{"message":"copy editing","shortMessageHtmlLink":"copy editing"}},{"before":null,"after":"de3a0819f1139f41482ae58029d6ae97a4d6dd9f","ref":"refs/heads/845-run-through-tutorial-using-10-release-1","pushedAt":"2024-04-29T19:47:58.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameseastwood","name":"James R. Baggs Eastwood","path":"/jameseastwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1616602?s=80&v=4"},"commit":{"message":"Fix old showcase for 1.0 release (#128)\n\n* spruce up CI\r\n\r\n* now test the rc\r\n\r\n* fix showcase notebook\r\n\r\n* small fixes\r\n\r\n* fix old showcase for 1.0\r\n\r\n* pull in from main channel now\r\n\r\n* update url for installer\r\n\r\n* some hacks to make colab work\r\n\r\n* add note explaining hack\r\n\r\n* fix missing imports\r\n\r\n* 1.0 api fixes\r\n\r\n---------\r\n\r\nCo-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>","shortMessageHtmlLink":"Fix old showcase for 1.0 release (#128)"}},{"before":"585310d33fd362984aeda18b3f45b3fa1150afad","after":null,"ref":"refs/heads/add_options_mappers_networks","pushedAt":"2024-04-26T13:05:28.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"hannahbaumann","name":"Hannah Baumann","path":"/hannahbaumann","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/43765638?s=80&v=4"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEP_86dgA","startCursor":null,"endCursor":null}},"title":"Activity · OpenFreeEnergy/ExampleNotebooks"}