{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":459646937,"defaultBranch":"main","name":"alchemiscale","ownerLogin":"openforcefield","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-02-15T15:54:42.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/18539698?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1715606468.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"ce41a1c3e31bb3a166e37b1d815569003d050ff4","ref":"refs/heads/fix-regex_query_nullfield","pushedAt":"2024-05-13T13:21:08.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Fixed the query_network method in `statestore.py`\n\nSince attributes of GufeTokenizables that are set to None are not\nexplicitly stored in the Neo4j database, regular expression fails to\nmatch nodes. Because of this, we no longer introduce wildcards when a\nattribute pattern is set to None. Instead, we completely remove that\nattribute regex condition from the WHERE clause.","shortMessageHtmlLink":"Fixed the query_network method in statestore.py"}},{"before":null,"after":"eb6a388a07decd8ebf9de58be6b34840d63afaba","ref":"refs/heads/add_nagl_and_espaloma_charge","pushedAt":"2024-05-07T15:48:31.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mikemhenry","name":"Mike Henry","path":"/mikemhenry","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11765982?s=80&v=4"},"commit":{"message":"Add espaloma_charge and nagl","shortMessageHtmlLink":"Add espaloma_charge and nagl"}},{"before":null,"after":"ff2a9b1b6158bfd08eb719f07fd8313bd361a0e2","ref":"refs/heads/docs-operation_fix","pushedAt":"2024-05-01T22:00:05.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Update operations manual in docs\n\nNeo4j 5.X introduced new subcommands for database management commands.\nThis commit reflects these changes with regards to dumping a database to\na file and adds a recommendation that the user renames the database dump\nfor archiving.","shortMessageHtmlLink":"Update operations manual in docs"}},{"before":"e79ab5ce19c96cb6b177add253728202c463fc3e","after":"8394a53f8bf529de9367022adc68d033ac1bd41c","ref":"refs/heads/test/openfe-gufe-1.0.0rc0","pushedAt":"2024-05-01T18:41:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Bumped alchemiscale to v0.4.1-beta.1 in conda envs\n\n* devtools/conda-envs/alchemiscale-client.yml\n* devtools/conda-envs/alchemiscale-compute.yml\n* devtools/conda-envs/alchemiscale-server.yml","shortMessageHtmlLink":"Bumped alchemiscale to v0.4.1-beta.1 in conda envs"}},{"before":"4a841942ea850e6fbe9dcfd196ef4eb49c342eb6","after":"e79ab5ce19c96cb6b177add253728202c463fc3e","ref":"refs/heads/test/openfe-gufe-1.0.0rc0","pushedAt":"2024-05-01T17:25:27.000Z","pushType":"push","commitsCount":85,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/main' into test/openfe-gufe-1.0.0rc0","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/main' into test/openfe-gufe-1.0.…"}},{"before":"383e473cd9ed4e97699e363a8bd0ef50ab7b376c","after":"3975cd459d5e81851ccd3d0bcc25ad517d4eccad","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-30T20:50:59.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Updated cache parameter handling in AlchemiscaleBaseClient\n\nThe AlchemiscaleBaseClient now determines the cache directory\nwhen one is not specified directly (i.e. a None is provided to the\nAlchemiscaleBaseClient constructor). When a path to this directory is\nprovided, it must be a string or pathlib.Path object. The logic for\nthis operation lies in the `AlchemiscaleBaseClient._determine_cache_dir`\nmethod, which can raise a TypeError on invalid input.\n\nThe `cache_size_limit` is now verified within the constructor to be\n>= 0. If it is not, then a ValueError is raised.\n\nNew tests have been added for the above changes:\n\n* Negative cache_size_limit: checks for constructor-raised ValueError\n with a meaningful message.\n\n* cache_directory is None: checks output of the underlying\n _determine_cache_dir method with and without the XDG_CACHE_HOME\n environment variable. If we test it with the client constructor, the\n directory is made automatically, which we don't want in the tests as\n it may touch real data.\n\n* cache_directory is not None, str, or Path: Check that the constructor\n raises a TypeError with a meaningful message.","shortMessageHtmlLink":"Updated cache parameter handling in AlchemiscaleBaseClient"}},{"before":"18c624839c8cf87a1bda49742d7f6208f2eff9d3","after":"383e473cd9ed4e97699e363a8bd0ef50ab7b376c","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-30T15:42:44.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Merge branch 'main' into feature-diskcache_integration","shortMessageHtmlLink":"Merge branch 'main' into feature-diskcache_integration"}},{"before":"dc9d32bea0edb135f38b904b10002116d514a204","after":"140e7eb4c5e0c3d92ad4fb0a1474f39a6ac3d3b0","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T15:37:13.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Merge branch 'main' into alchemiscale-fah","shortMessageHtmlLink":"Merge branch 'main' into alchemiscale-fah"}},{"before":"cda65755e38186aa41cd7987c216bf6bda063cee","after":null,"ref":"refs/heads/feature-more_httpexceptions","pushedAt":"2024-04-30T15:33:45.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"}},{"before":"88699d9697cedf52011609deee3a430c3fd5e5ce","after":"0954e32573d157271e565f488ccf72a61821bd58","ref":"refs/heads/main","pushedAt":"2024-04-30T15:33:38.000Z","pushType":"pr_merge","commitsCount":12,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Merge pull request #269 from openforcefield/feature-more_httpexceptions\n\nMore `HTTPException`s in the interface API endpoints","shortMessageHtmlLink":"Merge pull request #269 from openforcefield/feature-more_httpexceptions"}},{"before":"d54bc0bb76bb473ed963257708187dc361c6cb3f","after":"dc9d32bea0edb135f38b904b10002116d514a204","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T06:00:45.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Black!","shortMessageHtmlLink":"Black!"}},{"before":"25f91845f04cd85d3af48e9175d7de67f9562829","after":"d54bc0bb76bb473ed963257708187dc361c6cb3f","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T05:23:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Attempting to fix broken tests","shortMessageHtmlLink":"Attempting to fix broken tests"}},{"before":"f78d5adc641546fb7d76145138d8789f87e2da88","after":"25f91845f04cd85d3af48e9175d7de67f9562829","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T04:58:42.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Merge branch 'main' into alchemiscale-fah","shortMessageHtmlLink":"Merge branch 'main' into alchemiscale-fah"}},{"before":"1755f1f9451faca01faa7187c0c9213855818488","after":"f78d5adc641546fb7d76145138d8789f87e2da88","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T04:56:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Fix to statestore for broken tests","shortMessageHtmlLink":"Fix to statestore for broken tests"}},{"before":"6e12ba63cf41e7628432d543e48caee25c07cc7b","after":"1755f1f9451faca01faa7187c0c9213855818488","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-30T00:43:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Fixes to test suite","shortMessageHtmlLink":"Fixes to test suite"}},{"before":"b0d888ab8335b5962bd966938006cf3361c63629","after":"cda65755e38186aa41cd7987c216bf6bda063cee","ref":"refs/heads/feature-more_httpexceptions","pushedAt":"2024-04-29T22:19:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Updated exception handling for get_taskhub try block","shortMessageHtmlLink":"Updated exception handling for get_taskhub try block"}},{"before":"471faf984fd6e8c982f01c578a2d9cf659a5d832","after":"18c624839c8cf87a1bda49742d7f6208f2eff9d3","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-29T22:13:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Test cache data corruption and change test params\n\n* With known cached results, corrupt the values and make sure the user\n is warned that there was a problem with deserialization and that a\n new result will be downloaded.\n* Lowered the cache size limit for tests to avoid running out of space","shortMessageHtmlLink":"Test cache data corruption and change test params"}},{"before":"c9a0d78a4178fcc7ecc02b7f97860584699652de","after":"471faf984fd6e8c982f01c578a2d9cf659a5d832","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-29T19:55:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Enable caching for other objects\n\nNew objects supported:\n* Transformations\n* AlchemicalNetworks\n* ChemicalSystems\n* Generally anything that can be a KeyedChain","shortMessageHtmlLink":"Enable caching for other objects"}},{"before":"651a3faed3050e69fc7865b30a3974044a8ea980","after":"c9a0d78a4178fcc7ecc02b7f97860584699652de","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-29T16:54:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Clean up of the test_client.py file","shortMessageHtmlLink":"Clean up of the test_client.py file"}},{"before":null,"after":"651a3faed3050e69fc7865b30a3974044a8ea980","ref":"refs/heads/feature-diskcache_integration","pushedAt":"2024-04-25T21:29:07.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Use a diskcache.Cache to hold ProtocolDAGResults","shortMessageHtmlLink":"Use a diskcache.Cache to hold ProtocolDAGResults"}},{"before":"9bfd45821a0d0b40222f93059ec80a956fb154c5","after":"b0d888ab8335b5962bd966938006cf3361c63629","ref":"refs/heads/feature-more_httpexceptions","pushedAt":"2024-04-25T05:15:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Small edits on review from @dotsdl","shortMessageHtmlLink":"Small edits on review from @dotsdl"}},{"before":"77160dbef33ad13d9146500c666000d606416efe","after":"9bfd45821a0d0b40222f93059ec80a956fb154c5","ref":"refs/heads/feature-more_httpexceptions","pushedAt":"2024-04-24T04:49:51.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Merge branch 'main' into feature-more_httpexceptions","shortMessageHtmlLink":"Merge branch 'main' into feature-more_httpexceptions"}},{"before":"4181a8ceced8b69f8c26e8cb9de3a55bb35ef3e2","after":null,"ref":"refs/heads/feature-nontransformation_support","pushedAt":"2024-04-23T18:12:22.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"}},{"before":"42df32a26a386bfdf69da7646b0fdac7f90e200e","after":"88699d9697cedf52011609deee3a430c3fd5e5ce","ref":"refs/heads/main","pushedAt":"2024-04-23T18:12:17.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Merge pull request #270 from openforcefield/feature-nontransformation_support\n\nAdded support for `NonTransformation`s","shortMessageHtmlLink":"Merge pull request #270 from openforcefield/feature-nontransformation…"}},{"before":"70f72e7956db75a39133d7c9d8ee968b095502f7","after":"4181a8ceced8b69f8c26e8cb9de3a55bb35ef3e2","ref":"refs/heads/feature-nontransformation_support","pushedAt":"2024-04-23T17:50:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Removed unused import from validators.py","shortMessageHtmlLink":"Removed unused import from validators.py"}},{"before":"79a6c14c8545ed75c48542a1e277852b47b4eb23","after":"70f72e7956db75a39133d7c9d8ee968b095502f7","ref":"refs/heads/feature-nontransformation_support","pushedAt":"2024-04-18T17:30:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Make Transformation selection clearer in tests\n\n* Transformations are now sorted by their GufeKeys, and filter out\n NonTransformations when setting up n4js_preloaded actioned tasks.\n* `get_edge_type` helper method in integration/conftest.py also\n sorts by GufeKey so we know we are getting the same ordering","shortMessageHtmlLink":"Make Transformation selection clearer in tests"}},{"before":null,"after":"79a6c14c8545ed75c48542a1e277852b47b4eb23","ref":"refs/heads/feature-nontransformation_support","pushedAt":"2024-04-17T22:20:13.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Added support for NonTransformations\n\n- `network_tyk2` now includes NonTransformations\n on all ChemicalSystems\n- Added a helper method to\n `integration/conftest.py` to get the first\n instance of a Transformation or a\n NonTransformation\n- New fixture `nontransformation`\n- Updated Cypher queries relating to\n Transformations to `|` with\n NonTransformations","shortMessageHtmlLink":"Added support for NonTransformations"}},{"before":null,"after":"77160dbef33ad13d9146500c666000d606416efe","ref":"refs/heads/feature-more_httpexceptions","pushedAt":"2024-04-16T23:28:54.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"ianmkenney","name":"Ian Kenney","path":"/ianmkenney","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7085164?s=80&v=4"},"commit":{"message":"Added HTTPExceptions to API endpoints\n\n- `create_tasks`\n- `get_network_tasks`\n- `get_transformation_tasks`\n- `get_network_status`\n- `get_network_actioned_tasks`\n- `action_tasks`\n- `cancel_tasks`\n- `get_task_transformation`\n- `get_protocoldagresult`","shortMessageHtmlLink":"Added HTTPExceptions to API endpoints"}},{"before":"8e9281c73ddafdc83d976171758c7f12f4d1b4f8","after":"6e12ba63cf41e7628432d543e48caee25c07cc7b","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-16T05:36:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Getting errors from pytest for fixtures being registered as a plugin already","shortMessageHtmlLink":"Getting errors from pytest for fixtures being registered as a plugin …"}},{"before":"5b873b38fb7f2dafc0163ea368c3d78618da3a01","after":"8e9281c73ddafdc83d976171758c7f12f4d1b4f8","ref":"refs/heads/alchemiscale-fah","pushedAt":"2024-04-16T05:08:46.000Z","pushType":"push","commitsCount":67,"pusher":{"login":"dotsdl","name":"David L. Dotson","path":"/dotsdl","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1326811?s=80&v=4"},"commit":{"message":"Merge branch 'main' into alchemiscale-fah","shortMessageHtmlLink":"Merge branch 'main' into alchemiscale-fah"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAESG7x5QA","startCursor":null,"endCursor":null}},"title":"Activity · openforcefield/alchemiscale"}