{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":541210755,"defaultBranch":"main","name":"primaschema","ownerLogin":"pha4ge","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2022-09-25T15:08:42.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/50156331?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1724599634.0","currentOid":""},"activityList":{"items":[{"before":"7a4832591ed865e591c2bd9ef28cd6d1fab626d8","after":"e886defcc1822e827456e98993eee5d02d84e195","ref":"refs/heads/main","pushedAt":"2024-08-26T22:23:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Discard bed chrom field after first space during validation","shortMessageHtmlLink":"Discard bed chrom field after first space during validation"}},{"before":"d4d0591f2c0d562b9dd1535cec9b5ef3ba83fc8b","after":"7a4832591ed865e591c2bd9ef28cd6d1fab626d8","ref":"refs/heads/main","pushedAt":"2024-08-26T21:34:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Use JSON for schemes manifest (#55)","shortMessageHtmlLink":"Use JSON for schemes manifest (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2486702806\" data-permission-text=\"Title is private\" data-url=\"https://github.com/pha4ge/primaschema/issues/55\" data-hovercard-type=\"issue\" data-hovercard-url=\"/pha4ge/primaschema/issues/55/hovercard\" href=\"https://github.com/pha4ge/primaschema/issues/55\">#55</a>)"}},{"before":"1f811d9ede67684b130be43eb1a27191a5a26cef","after":"d4d0591f2c0d562b9dd1535cec9b5ef3ba83fc8b","ref":"refs/heads/main","pushedAt":"2024-08-25T15:56:27.000Z","pushType":"pr_merge","commitsCount":5,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Merge pull request #54 from pha4ge/add_region_mask\n\nAdd region mask to model (follow up to #52)","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2485346640\" data-permission-text=\"Title is private\" data-url=\"https://github.com/pha4ge/primaschema/issues/54\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/pha4ge/primaschema/pull/54/hovercard\" href=\"https://github.com/pha4ge/primaschema/pull/54\">#54</a> from pha4ge/add_region_mask"}},{"before":null,"after":"935b740da5dabbc4b56dc221249a3218c6bef948","ref":"refs/heads/add_region_mask","pushedAt":"2024-08-25T15:27:14.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Sync test data with scheme repo to pass tests, make vendor url optional","shortMessageHtmlLink":"Sync test data with scheme repo to pass tests, make vendor url optional"}},{"before":"b583cc49b4095be2b7a9c75dbdef18b87c99a6f3","after":"1f811d9ede67684b130be43eb1a27191a5a26cef","ref":"refs/heads/main","pushedAt":"2024-08-22T12:31:40.000Z","pushType":"pr_merge","commitsCount":57,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Merge pull request #51 from pha4ge/v1a\n\nMerge v1a (1.0.0a0) into main","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2480667708\" data-permission-text=\"Title is private\" data-url=\"https://github.com/pha4ge/primaschema/issues/51\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/pha4ge/primaschema/pull/51/hovercard\" href=\"https://github.com/pha4ge/primaschema/pull/51\">#51</a> from pha4ge/v1a"}},{"before":"5a2c9e446371deb1795d6b0428a428ceaf19df9c","after":"2ce3b397838d66346ee32c5b73af7789d50e7c6a","ref":"refs/heads/v1a","pushedAt":"2024-08-22T12:31:21.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Merge branch 'main' into v1a","shortMessageHtmlLink":"Merge branch 'main' into v1a"}},{"before":"5a92dab3c0ab6b993f885dc6c409373dea6bbf01","after":"5a2c9e446371deb1795d6b0428a428ceaf19df9c","ref":"refs/heads/v1a","pushedAt":"2024-08-22T12:27:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Add warning to readme","shortMessageHtmlLink":"Add warning to readme"}},{"before":"8d38b564b19d1dd25263e8914057523e08311c88","after":"5a92dab3c0ab6b993f885dc6c409373dea6bbf01","ref":"refs/heads/v1a","pushedAt":"2024-08-22T12:11:40.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Update readme","shortMessageHtmlLink":"Update readme"}},{"before":"7bb3875106f1b2d5a9982124eddd8ca6a61e7dbc","after":"8d38b564b19d1dd25263e8914057523e08311c88","ref":"refs/heads/v1a","pushedAt":"2024-08-21T21:29:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Drop requirement for scheme bed in discordant_primers()","shortMessageHtmlLink":"Drop requirement for scheme bed in discordant_primers()"}},{"before":"24f5294ed8a6689c1ce968aa0ed01188323a9820","after":"7bb3875106f1b2d5a9982124eddd8ca6a61e7dbc","ref":"refs/heads/v1a","pushedAt":"2024-08-20T23:30:57.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"primaschema subset: extract single chrom subset primer.bed and\nreference.fasta from a multi-chrom scheme definition","shortMessageHtmlLink":"primaschema subset: extract single chrom subset primer.bed and"}},{"before":"7ecd93767c1b5913721e68385cddd2d97c68d7ca","after":"24f5294ed8a6689c1ce968aa0ed01188323a9820","ref":"refs/heads/v1a","pushedAt":"2024-08-20T23:28:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"primaschema subset: extract single chrom subset primer.bed and reference.fasta from multi chrom scheme definition","shortMessageHtmlLink":"primaschema subset: extract single chrom subset primer.bed and refere…"}},{"before":"6b74b21b29674b1d45c60c5fa8c4c87e9f7f0081","after":"7ecd93767c1b5913721e68385cddd2d97c68d7ca","ref":"refs/heads/v1a","pushedAt":"2024-08-20T14:01:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Use tarball instead","shortMessageHtmlLink":"Use tarball instead"}},{"before":"3df90431319b0227ba8b7bf16668da60bebc6bf0","after":"6b74b21b29674b1d45c60c5fa8c4c87e9f7f0081","ref":"refs/heads/v1a","pushedAt":"2024-08-20T12:59:27.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"primaschema sync: synchronise local copy of remote primer schemes repository","shortMessageHtmlLink":"primaschema sync: synchronise local copy of remote primer schemes rep…"}},{"before":"2de86270d4df4822e5d2ea833932310939ed8654","after":"3df90431319b0227ba8b7bf16668da60bebc6bf0","ref":"refs/heads/v1a","pushedAt":"2024-08-12T17:26:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Synchronise stub","shortMessageHtmlLink":"Synchronise stub"}},{"before":"52e4f96ce260ec145a9bb722b78053ac7a115145","after":"2de86270d4df4822e5d2ea833932310939ed8654","ref":"refs/heads/v1a","pushedAt":"2024-08-12T16:55:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"More consistent library function and subcommand naming","shortMessageHtmlLink":"More consistent library function and subcommand naming"}},{"before":"6a4f82b1305554b1b1100ff37c61dfdd977c7343","after":"52e4f96ce260ec145a9bb722b78053ac7a115145","ref":"refs/heads/v1a","pushedAt":"2024-08-12T16:35:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Remove hacks for Eden","shortMessageHtmlLink":"Remove hacks for Eden"}},{"before":"2d95d19258f6b1ba7799857ee9a1ffbc44237976","after":"6a4f82b1305554b1b1100ff37c61dfdd977c7343","ref":"refs/heads/v1a","pushedAt":"2024-08-12T16:12:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Use Pydantic model for info.yml parsing, python>=3.8 compatibility","shortMessageHtmlLink":"Use Pydantic model for info.yml parsing, python&gt;=3.8 compatibility"}},{"before":"b7702611c4b17822a37ea1aa642e8a180dffc383","after":"2d95d19258f6b1ba7799857ee9a1ffbc44237976","ref":"refs/heads/v1a","pushedAt":"2024-08-06T17:00:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Reimplement faster info yaml validation with Pydantic rather than LinkML\n\nMoved schema into pkg dir (automatic distribution with flit)\nLots of tidying\nAdds tests","shortMessageHtmlLink":"Reimplement faster info yaml validation with Pydantic rather than LinkML"}},{"before":"7f8a10f463707edf141403c2b23e63b1fe6013ce","after":"b7702611c4b17822a37ea1aa642e8a180dffc383","ref":"refs/heads/v1a","pushedAt":"2024-08-05T16:56:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"primaschema build plots by default","shortMessageHtmlLink":"primaschema build plots by default"}},{"before":"57d5bb9379473d29a5395fb23a4d3bc3bcae136e","after":"7f8a10f463707edf141403c2b23e63b1fe6013ce","ref":"refs/heads/v1a","pushedAt":"2024-08-05T16:43:38.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Combine validate and validate-recursive","shortMessageHtmlLink":"Combine validate and validate-recursive"}},{"before":"b139050aa8d19918b79fb587a77888fcd1ccfa12","after":"57d5bb9379473d29a5395fb23a4d3bc3bcae136e","ref":"refs/heads/v1a","pushedAt":"2024-08-03T09:35:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Add new test data","shortMessageHtmlLink":"Add new test data"}},{"before":"b05f55d2b1069365167153f4cfcfe9f262023567","after":"b139050aa8d19918b79fb587a77888fcd1ccfa12","ref":"refs/heads/v1a","pushedAt":"2024-08-01T16:10:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Sort output BEDs in compatible format, related churn, and tests\n\nIntegrated sorting by amplicon name needed for ampliconstats compat","shortMessageHtmlLink":"Sort output BEDs in compatible format, related churn, and tests"}},{"before":"fec1ba5e0b2298cffcf877a570f4926e4320e1af","after":"b05f55d2b1069365167153f4cfcfe9f262023567","ref":"refs/heads/v1a","pushedAt":"2024-08-01T14:24:55.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Improved BED validation\n\nValidates BED and amplicon tiling for one or more reference\nchromosomes. Rejects complex tiling and duplicate primer names.\n\nVerifies that reference chroms in primer.bed exist in\nreference.fasta and they have sane coordinates.\n\nFixes bug in build-recursive and validate-recursive where schemes of\ndifferent version would clobber one another\n\nFixes primer and reference checksums for multi-chromosome refs.","shortMessageHtmlLink":"Improved BED validation"}},{"before":"1df1c7f37d7b2768460316ea2e0840d91a9bb386","after":"b05f55d2b1069365167153f4cfcfe9f262023567","ref":"refs/heads/validate-bed","pushedAt":"2024-08-01T14:05:40.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Improved BED validation\n\nValidates BED and amplicon tiling for one or more reference\nchromosomes. Rejects complex tiling and duplicate primer names.\n\nVerifies that reference chroms in primer.bed exist in\nreference.fasta and they have sane coordinates.\n\nFixes bug in build-recursive and validate-recursive where schemes of\ndifferent version would clobber one another\n\nFixes primer and reference checksums for multi-chromosome refs.","shortMessageHtmlLink":"Improved BED validation"}},{"before":null,"after":"1df1c7f37d7b2768460316ea2e0840d91a9bb386","ref":"refs/heads/validate-bed","pushedAt":"2024-07-31T14:24:25.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Rigorously validate BED contents including amplicon tiling using Pydantic model","shortMessageHtmlLink":"Rigorously validate BED contents including amplicon tiling using Pyda…"}},{"before":"0cf67a879dd76e0b8e6a0d3d43955e761ebe126f","after":"fec1ba5e0b2298cffcf877a570f4926e4320e1af","ref":"refs/heads/v1a","pushedAt":"2024-07-26T15:12:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Save vertical space by plotting poolName on y, fix poolName in test data","shortMessageHtmlLink":"Save vertical space by plotting poolName on y, fix poolName in test data"}},{"before":"d37c689043dd353597743157b44435864a94d4c7","after":"0cf67a879dd76e0b8e6a0d3d43955e761ebe126f","ref":"refs/heads/v1a","pushedAt":"2024-07-26T00:10:56.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Tidy tests, move primer-schemes test assets into test/data","shortMessageHtmlLink":"Tidy tests, move primer-schemes test assets into test/data"}},{"before":"e8d7986f485e2c1b97dfb7ab0f0c6dd94cb84a8e","after":"d37c689043dd353597743157b44435864a94d4c7","ref":"refs/heads/v1a","pushedAt":"2024-07-26T00:05:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Tidy tests, move primer-schemes test assets into test/data","shortMessageHtmlLink":"Tidy tests, move primer-schemes test assets into test/data"}},{"before":"fb3bda3906df28d20466a798daba831e692abd75","after":"e8d7986f485e2c1b97dfb7ab0f0c6dd94cb84a8e","ref":"refs/heads/v1a","pushedAt":"2024-07-25T23:31:16.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Test CI fix for path issue","shortMessageHtmlLink":"Test CI fix for path issue"}},{"before":"c2069e95f4aee3cebc29905539cbfede8c949865","after":"fb3bda3906df28d20466a798daba831e692abd75","ref":"refs/heads/v1a","pushedAt":"2024-07-25T23:24:37.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"bede","name":"Bede Constantinides","path":"/bede","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1007616?s=80&v=4"},"commit":{"message":"Debug CI path issue","shortMessageHtmlLink":"Debug CI path issue"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEpL1ClgA","startCursor":null,"endCursor":null}},"title":"Activity · pha4ge/primaschema"}