{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":51561527,"defaultBranch":"master","name":"pyontutils","ownerLogin":"tgbugs","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2016-02-12T01:55:32.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/4299776?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1726293990.0","currentOid":""},"activityList":{"items":[{"before":"c452e6af40b6bb20241748aac2722d655dc06d59","after":"49be71bd21807a8df0a3387ab797e9ffc5138f43","ref":"refs/heads/ibnode-v3","pushedAt":"2024-09-20T23:16:03.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"start of work on ibnode v3 to fix issues with\n\nlots of notes in here at the moment that need to be cleaned up becuase\nthey include in process thinking, much of which is incorrect\n\nthe major remaining bug to resolve has to do with the identities of\nlists and sublists\n\notherwise the biggest change so far is to use the identity of the list\nof pairs as the id for the whole object so that IdentityBNode could in\nprinciple be called recursively, still not quite there yet though\n\nmore detailed notes on changes will come once everything is fixed and\na bunch of the comments are cleaned up","shortMessageHtmlLink":"start of work on ibnode v3 to fix issues with"}},{"before":"71099bf3665449cc30aad891f20774326a4c3b6b","after":"b950423915315f3c9ae91a1de0aab63f2a308e37","ref":"refs/heads/master","pushedAt":"2024-09-20T01:57:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"phenotype edges update subPropertyOf for sensory axon ending","shortMessageHtmlLink":"phenotype edges update subPropertyOf for sensory axon ending"}},{"before":"2201c4592510c6cb8d556655ed35b31c726ce832","after":"71099bf3665449cc30aad891f20774326a4c3b6b","ref":"refs/heads/master","pushedAt":"2024-09-20T01:49:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurons apinat npo handle axon to sensory","shortMessageHtmlLink":"neurons apinat npo handle axon to sensory"}},{"before":"049dfb383d739b930b50ea0d9968db3d4b4774c4","after":"c452e6af40b6bb20241748aac2722d655dc06d59","ref":"refs/heads/ibnode-v3","pushedAt":"2024-09-19T22:56:10.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"start of work on ibnode v3 to fix issues with\n\nlots of notes in here at the moment that need to be cleaned up becuase\nthey include in process thinking, much of which is incorrect\n\nthe major remaining bug to resolve has to do with the identities of\nlists and sublists\n\notherwise the biggest change so far is to use the identity of the list\nof pairs as the id for the whole object so that IdentityBNode could in\nprinciple be called recursively, still not quite there yet though\n\nmore detailed notes on changes will come once everything is fixed and\na bunch of the comments are cleaned up","shortMessageHtmlLink":"start of work on ibnode v3 to fix issues with"}},{"before":"b30a8a62f6a99645aa63778e0509672572c57b84","after":"2201c4592510c6cb8d556655ed35b31c726ce832","ref":"refs/heads/master","pushedAt":"2024-09-19T22:55:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm npo include partial orders terms, nlp fix label, sens axons","shortMessageHtmlLink":"neurondm npo include partial orders terms, nlp fix label, sens axons"}},{"before":null,"after":"049dfb383d739b930b50ea0d9968db3d4b4774c4","ref":"refs/heads/ibnode-v3","pushedAt":"2024-09-14T06:06:30.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"start of work on ibnode v3 to fix issues with\n\nlots of notes in here at the moment that need to be cleaned up becuase\nthey include in process thinking, much of which is incorrect\n\nthe major remaining bug to resolve has to do with the identities of\nlists and sublists\n\notherwise the biggest change so far is to use the identity of the list\nof pairs as the id for the whole object so that IdentityBNode could in\nprinciple be called recursively, still not quite there yet though\n\nmore detailed notes on changes will come once everything is fixed and\na bunch of the comments are cleaned up","shortMessageHtmlLink":"start of work on ibnode v3 to fix issues with"}},{"before":"a97b191578d745d2d15cdf2d40e2843bc27d27a9","after":"b30a8a62f6a99645aa63778e0509672572c57b84","ref":"refs/heads/master","pushedAt":"2024-09-11T00:39:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm pcl updated to use neurdf\n\nlots of gene symbols are missed now","shortMessageHtmlLink":"neurondm pcl updated to use neurdf"}},{"before":"c105300ef5d38d62b735053b276e099353d38be5","after":"a97b191578d745d2d15cdf2d40e2843bc27d27a9","ref":"refs/heads/master","pushedAt":"2024-09-10T23:44:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"phenotype edges add axon leads to sensory","shortMessageHtmlLink":"phenotype edges add axon leads to sensory"}},{"before":"1ecea331d257ca025fff9e9231e43a5853878d40","after":"c105300ef5d38d62b735053b276e099353d38be5","ref":"refs/heads/master","pushedAt":"2024-09-05T00:06:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm test neurdf easier debug capture","shortMessageHtmlLink":"neurondm test neurdf easier debug capture"}},{"before":"afcbeb5b614e583133fece33cf5e951ed6fc7383","after":"1ecea331d257ca025fff9e9231e43a5853878d40","ref":"refs/heads/master","pushedAt":"2024-09-05T00:02:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm build exclude cut_development_raw","shortMessageHtmlLink":"neurondm build exclude cut_development_raw"}},{"before":"acc9455d5400e68a5824ff2f795e30a5115a0616","after":"afcbeb5b614e583133fece33cf5e951ed6fc7383","ref":"refs/heads/master","pushedAt":"2024-09-05T00:00:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm neurdf ser add support for subset of logical phenotypes\n\nthe subset supported covers all extant neurons, the support does break\nroundtripping since it flattens logical and up to the top intersection\nclass and converts logical or to UnionOf, which fact++ can prove is\nequivalent but elk can not","shortMessageHtmlLink":"neurondm neurdf ser add support for subset of logical phenotypes"}},{"before":"e339988c409767c37c2a73f234b51b37140e5d63","after":"acc9455d5400e68a5824ff2f795e30a5115a0616","ref":"refs/heads/master","pushedAt":"2024-09-04T19:28:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm first pass a neurdf serialization\n\nmissing support for logical phenotypes and nested owl objects,\notherwise is mostly working, there are a number of details that need\nto be worked out, but as expected the conversion is a straight forward\nmapping of predicates to a variety of prefix namespaces so that it\nwill be possible to map back to the original python\nrepresentation (though the lifting rules from neurdf to owl could also\nbe implemented directly)\n\nquerying over simple cases is easy, however when we get into the\nnegative and entailed cases and the owl objects things will not be so\nsimple, and there are more complex type specifications that what I\ncurrently produce for conversion from sparc nlp, so that should be\nkept in mind for current downstream consumers of simple sckan","shortMessageHtmlLink":"neurondm first pass a neurdf serialization"}},{"before":"78040ab22d1d33ea250c7da8c737b558af3639d7","after":"e339988c409767c37c2a73f234b51b37140e5d63","ref":"refs/heads/master","pushedAt":"2024-09-04T04:53:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"integration test helper updated to use find_spec\n\nthe change appears to be backward compatible all the way back to 3.6\nbased on testing on 3.6 and 3.7, it looks like iter_modules changed\nbetween 3.5 and 3.6 so 3.5 was already not supported\n\nideally this would not use pkgutil at all","shortMessageHtmlLink":"integration test helper updated to use find_spec"}},{"before":"6eeb48495df00ddefcc64e2f27336a6104b5f789","after":"78040ab22d1d33ea250c7da8c737b558af3639d7","ref":"refs/heads/master","pushedAt":"2024-09-04T03:14:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm vbump for release","shortMessageHtmlLink":"neurondm vbump for release"}},{"before":"185a206f859eeadd8b3d002cc7ec95304e619e1e","after":"6eeb48495df00ddefcc64e2f27336a6104b5f789","ref":"refs/heads/master","pushedAt":"2024-09-04T03:00:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm finish roundtrip for OwlObjects and also Entailed\n\ntests added for all the basic combinations along the axes for ttl/py,\nPos/Neg, Eqv/Ent, Id/Obj/Nst\n\nUnionOf, IntersectionOf, and IntersectionOfPartOf have been added to\nneurondm.lang.__all__, not sure whether IntersectionOfPartOf should be\nthere since it is inferred by the use of a location predicate, the\nargument for inclusion is that future plans for neurondm.simple\nwill no longer require a copy of an ontology for basic operations\n\nadd a temporary hacked fix to ensure that the internal representation\nfor ids inside OwlObjects is normalized (i.e. expanded), the big TODO\nhere is that Config is going to be changed to require the presence of\nlocal conventions so they are no longer implicit and dependent on the\nconfiguration state of pyontutils, will need an upgrade path to\nreserialize the implicit conventions, so add explicit config version\n\nfix load_python so that it will always reload a module at the same\npathname since the written config could be modified by hand or during\nthe course of repeated tests using the same file\n\nadd a note on switching to use frozenset for hashing instead of a\nsorted list to avoid the need to implement stable sort for all things\nthat combine to for pes\n\nfix phenotype __expanded__ to prevent spurious quotes\n\nbetter support for offline testing and usage when have local repo","shortMessageHtmlLink":"neurondm finish roundtrip for OwlObjects and also Entailed"}},{"before":"0d16934ea81c9dd2bde2d25f64a072676e2f3423","after":"185a206f859eeadd8b3d002cc7ec95304e619e1e","ref":"refs/heads/master","pushedAt":"2024-08-29T07:12:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm owl object start on roundtrip tests\n\nthis the skeleton in place should be able to converge fairly quickly\n\nthis commit intentionally introduces a failing test\n\nlots of stuff to work through here, made a few initial tweaks so that\nwe can at least get to a test failure instead of an error, though\nthere will be many more errors as I work on proper conversion back\nfrom owl to python (sigh the awfulness of the impl again ...)","shortMessageHtmlLink":"neurondm owl object start on roundtrip tests"}},{"before":"e6a66ccb372777705c2dee2a9d499ba7964cd818","after":"0d16934ea81c9dd2bde2d25f64a072676e2f3423","ref":"refs/heads/master","pushedAt":"2024-08-29T05:42:29.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm owl object add tests for entailed phenotype cases","shortMessageHtmlLink":"neurondm owl object add tests for entailed phenotype cases"}},{"before":"999404fd55cabb0b8edf10e3b9aaab00b1ccb4cc","after":"e6a66ccb372777705c2dee2a9d499ba7964cd818","ref":"refs/heads/master","pushedAt":"2024-08-27T20:15:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm build update skip for swglnd","shortMessageHtmlLink":"neurondm build update skip for swglnd"}},{"before":"8ddfa0d31bf2191e45e275b3ee149b3ea09e4a71","after":"999404fd55cabb0b8edf10e3b9aaab00b1ccb4cc","ref":"refs/heads/master","pushedAt":"2024-08-27T19:38:42.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"ontload prov actually parse --nowish arg to a datetime object","shortMessageHtmlLink":"ontload prov actually parse --nowish arg to a datetime object"}},{"before":"6bba396f5b1a6d1834994d3a9b8825c1dc595c23","after":"8ddfa0d31bf2191e45e275b3ee149b3ea09e4a71","ref":"refs/heads/master","pushedAt":"2024-08-21T01:42:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm yield bad superclasses unless another option exists\n\ntrying to avoid the stupid BFO:0000002 and BFO:0000040 behavior","shortMessageHtmlLink":"neurondm yield bad superclasses unless another option exists"}},{"before":"cc91bf6ef54c4f3972ba65c8b6368d64c6c5aa48","after":"6bba396f5b1a6d1834994d3a9b8825c1dc595c23","ref":"refs/heads/master","pushedAt":"2024-08-21T00:42:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm build workaround for hasPart partOf issue\n\na hasPart b does not actually imply b partOf a for all b, it implies\ninstead that there exists some subClassOf b for which scob partOf a\n\nas such we need to remove the hardcoded known_inverses in ontquery and\npyontutils, but for now we go with this fix instead\n\nalso prevent other curation sets from being pulled in","shortMessageHtmlLink":"neurondm build workaround for hasPart partOf issue"}},{"before":"55b89f961979b55e2bc55c9646b8174e929e675c","after":"cc91bf6ef54c4f3972ba65c8b6368d64c6c5aa48","ref":"refs/heads/master","pushedAt":"2024-08-07T01:03:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"update curie map for new sckan sets and add note","shortMessageHtmlLink":"update curie map for new sckan sets and add note"}},{"before":"223825e717b3ac0c783d64b1f23c61df1fb07581","after":"55b89f961979b55e2bc55c9646b8174e929e675c","ref":"refs/heads/master","pushedAt":"2024-08-03T20:07:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"pyontutils core fix regex escapes","shortMessageHtmlLink":"pyontutils core fix regex escapes"}},{"before":"0f57bd661fd8b64faab7ec3dd4d652d95897805e","after":"223825e717b3ac0c783d64b1f23c61df1fb07581","ref":"refs/heads/master","pushedAt":"2024-08-03T03:24:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"sheets only run auth flow if refresh errors out\n\nstale creds file structure can cause this to happen, otherwise we\ndon't want to run the full flow every time since it is almost never\nneeded, also don't open the browser automatically","shortMessageHtmlLink":"sheets only run auth flow if refresh errors out"}},{"before":"5203a2ed4b404e82ccc1f8cb29bee093933b9125","after":"0f57bd661fd8b64faab7ec3dd4d652d95897805e","ref":"refs/heads/master","pushedAt":"2024-08-03T02:11:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"sheets updated google auth flow to current conventions\n\napparently refresh doesn't work and run_console is long deprecated\nmostly should be using the service account file but this still needs\nto work as expected","shortMessageHtmlLink":"sheets updated google auth flow to current conventions"}},{"before":"c3f96e8a9b34c52a955522dc12df01ddf01e31ba","after":"5203a2ed4b404e82ccc1f8cb29bee093933b9125","ref":"refs/heads/master","pushedAt":"2024-08-01T23:04:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm nlp add kidney and liver\n\nalso fail over to use structure name for id if id is missing when\ndebug is set to true","shortMessageHtmlLink":"neurondm nlp add kidney and liver"}},{"before":"3fe47bb0609920f76359470a510be63d79843a0a","after":"c3f96e8a9b34c52a955522dc12df01ddf01e31ba","ref":"refs/heads/master","pushedAt":"2024-06-11T09:06:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm nlp first pass at sensory motor","shortMessageHtmlLink":"neurondm nlp first pass at sensory motor"}},{"before":"e4cedae73239e56538dd498dbf39ee0d7e0c6cfa","after":"3fe47bb0609920f76359470a510be63d79843a0a","ref":"refs/heads/master","pushedAt":"2024-03-06T01:36:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"scr sync updated to correctly populate replacedBy\n\nsome records marked as Rejected are actually deprecated and are\nreplaced by another SCR id, we maintain the mapping here but have to\ncreate a lookup table to distinguish between cases where a record was\nactually deprecated vs simply rejected\n\nin the process added a new warning if we detect cases where the same\naltnerative id is associated with multiple distinct scr ids","shortMessageHtmlLink":"scr sync updated to correctly populate replacedBy"}},{"before":"eafd685740e5bf99f19c8ed0548e7c920bef7399","after":"e4cedae73239e56538dd498dbf39ee0d7e0c6cfa","ref":"refs/heads/master","pushedAt":"2024-03-04T18:30:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm nlp tweaks for femrep","shortMessageHtmlLink":"neurondm nlp tweaks for femrep"}},{"before":"30c415207b11644808f70c8caecc0c75bd6acb0a","after":"eafd685740e5bf99f19c8ed0548e7c920bef7399","ref":"refs/heads/master","pushedAt":"2024-01-05T18:51:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"tgbugs","name":"Tom Gillespie","path":"/tgbugs","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4299776?s=80&v=4"},"commit":{"message":"neurondm vbump for release","shortMessageHtmlLink":"neurondm vbump for release"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yMFQyMzoxNjowMy4wMDAwMDBazwAAAAS8bwYO","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMS0wNVQxODo1MTozMi4wMDAwMDBazwAAAAPY0roT"}},"title":"Activity ยท tgbugs/pyontutils"}