Clinical-Genomics / scout

Коли додано кожну зірку й форк — зібрано з GitHub і згруповано за днями. Кумулятивне зростання розміщено просто над денними додаваннями, з яких воно складається, тож їх видно одне проти одного: рівномірне органічне накопичення виглядає зовсім інакше, ніж різкий короткочасний сплеск. Там, де цю різницю можна виміряти, її подано як автентичність росту.

Кожна точка охоплює 11 днів.

Повний розв'язаний набір залежностей із графа залежностей GitHub: 36 прямих і 82 непрямих (транзитивних) пакетів. Транзитивне замикання є повним, коли в репозиторії закомічено lockfile.

Цей репозиторій не публікує пакета, який розпізнає індекс, тож оцінено його власний граф залежностей — 118 пакетів, серед яких є й піниї розробки та тестування, що ніколи не постачаються: 1 мають відомі сповіщення, з них 1 прямі.

Сповіщення означає, що версія, записана в графі залежностей, потрапляє в уражений діапазон. Досяжність не аналізується, а граф містить піниї розробки й тестування — знахідка може стосуватися інструментів, а не поставленого коду.

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          "body": "* Make comments editable/removable by LDAP users\n\n* Forgot to add the file\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Make comments editable/removable by LDAP users (#6439)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-24T07:44:02Z",
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          "oid": "66315ec24500162f28ab4ceab6bbb2897d641306",
          "body": "* Fix #6436 - `CN=.` call parsing issue\n\n* nope. Debug!\n\n* ah, perhaps the numpy array value is already nan\n\n* add nan detection\n\n* add a docstring",
          "is_bot": false,
          "headline": "Fix #6436 - `CN=.` call parsing issue (#6437)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-24T07:36:13Z",
          "body_truncated": false,
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        {
          "oid": "aa755930e5292c0df7f153319cb350743e0a5588",
          "body": "…n admin (#6416)\n\n* Institute-level dismiss variants tahs\n\n* Display selected items on institute settings\n\n* PR ref in changelog\n\n* Remove logging messages\n\n* Thanks SonarCloud\n\n* How about this\n\n* Tiny fix\n\n* Other fix\n\n* Removed a couple of commas\n\n* Apply the same on variant page\n\n* Small fix\n\n* Add a test\n\n* Revert ID of form element\n\n* Fix according to review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Customise displayed variant dismiss tags in institute settings - as a…",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-23T12:15:42Z",
          "body_truncated": false,
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        {
          "oid": "0a0f5324a04a5272ee63ad7adfc969b59f5e8dbd",
          "body": "* Fix error in typing on adapter acmg module\n\n* Fix one more of the same\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Fix error in typing on adapter acmg module (#6433)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-23T07:57:40Z",
          "body_truncated": false,
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          "oid": "984cc64fad84a9f0ed382936226f7889d7c7f872",
          "body": "…ants (#6430)\n\n* Fix #6428 - GnomAD MT link out from empty r2 to r3/r4 build with variants\n\n* Fix #6431 - de-duplicate MT links\n\n* convince sonarcloud\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6428 - GnomAD MT link out from empty r2 to r3/r4 build with vari…",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-23T07:49:32Z",
          "body_truncated": false,
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        {
          "oid": "226d7e8f9f9aeacaf445a4de82180e1f67baf99b",
          "body": "* Hide variants with no GT call on MT reports\n\n* Remove unused import and add PR ref\n\n* Explicit skip variant\n\n* Apply suggestion from @dnil\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Fix code style issues with Black\n\n* Use a common constant\n\n* Rename constant\n\n* Reduce complexity\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>",
          "is_bot": false,
          "headline": "Hide variants with no GT call on MT reports (#6429)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-22T13:08:29Z",
          "body_truncated": false,
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          "oid": "8b8095683d578e091c9ad3b49209fef87fe524a0",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6425 - sort external gene links esp litvar2 link (#6426)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-22T08:28:08Z",
          "body_truncated": false,
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          "oid": "0166a184a5312dc437e14a43aabc890915826793",
          "body": "* Moved liftover mocked responses to conftests\n\n* Small fix\n\n* Changelog ref\n\n* json to dict\n\n* Fixed changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Moved liftover mocked responses to conftest (#6415)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-18T14:11:29Z",
          "body_truncated": false,
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        {
          "oid": "d5b1686e3df32d3f9c8f95eaa00a8e41d472bf74",
          "body": "* Display 2 GnomAD frequency links on SNV and Gene pages\n\n* Small fixes\n\n* Safer code\n\n* Do not repeat gene links 4 times\n\n* Just one gene link\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Display 2 GnomAD frequency links on SNV and Gene pages (#6413)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-18T13:57:42Z",
          "body_truncated": false,
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          "oid": "a8127e21af53d19b09905e0b6b226807de56fd6c",
          "body": "* Fix #6392 - NA for missing GQ. TypeHint for ACMG evaluation criterion.\n\n* Changelog\n\n* Bump Changelog PR nr\n\n* Update scout/models/acmg_evaluation.py\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Missing gq na (#6420)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-18T12:12:19Z",
          "body_truncated": false,
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          "oid": "3dc3fd78d969c935f84333030459539a4891a6fb",
          "body": "* Same icon on case page\n\n* Updated changelog\n\n* Fix changelog\n\n* Group icon only if more than one sample\n\n* Revert the config\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Clearer gens buttons on SV variant page (#6410)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-18T07:23:46Z",
          "body_truncated": false,
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          "oid": "0007b902d9810638b8db7149db0a06421b108063",
          "body": "* ACMG evaluation page doesn't close after submission\n\n* Import missing modules\n\n* Add PR ref\n\n* Fixed clearing ACMG without criterua\n\n* Fix syntax in test\n\n* Small fix for return type\n\n* Same fix in other function\n\n* Use fake model for criteria and fix type hint\n\n* Introduced double button, to optionally redirect\n\n* Updated changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Keep ACMG classification open after submit (#6405)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-18T05:58:46Z",
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          "body": "Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Normalise email/id field to lowercase when using LDAP login (#6407)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-15T09:31:21Z",
          "body_truncated": false,
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        {
          "oid": "3d6b1e5d4e6f82301538f5d6a95dcb99883da972",
          "body": "* Normalize new users' emails when created by GUI\n\n* Fix test\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Normalize new users' emails when created by GUI (#6406)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-15T09:24:26Z",
          "body_truncated": false,
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        {
          "oid": "b2f3d6986251d5d5948e24da03dcdcf995214358",
          "body": "* Fix #6363 - comments accept markdown syntax\n\n* Update changelog PR nr\n\n* Update changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6363 - comments accept markdown syntax (#6401)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-15T09:14:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0fb3acb74d56807299b3c85243bb16fcc8c77c51",
          "body": "* Compare LDAP auth response against enum\n\n* Update PR number",
          "is_bot": false,
          "headline": "Compare LDAP auth response against enum (#6400)",
          "author_name": "Alexander Koc",
          "author_login": "alkc",
          "committed_at": "2026-06-15T07:14:39Z",
          "body_truncated": false,
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        {
          "oid": "5e266273a674f790fdb002d1c7d40e3e81e35ab5",
          "body": "* Fix links in causatives exported to managed variants format\n\n* Remove debug messages\n\n* Even better fix\n\n* Rename one more\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix links in causatives exported to managed variants format (#6398)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-12T12:50:34Z",
          "body_truncated": false,
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        },
        {
          "oid": "ebcb6515389c735bc0b5e5809284da0fa08c1bdc",
          "body": "* Fix exporting causatives from 38 cases without --build param\n\n* Fix before\n\n* Same length in tuple\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix exporting causatives from 38 cases without --build param (#6399)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-12T12:11:09Z",
          "body_truncated": false,
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          "oid": "436007c98c0938376b3b8fdd6fdcb6ef5d825c00",
          "body": "…reas (#6390)\n\n* Fix PDF export to support multi-page output\n\n* Remove empty lines\n\n* PR ref in changelog\n\n* Reintroduce textarea text wrapping\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Fix ACMG PDF export to support multi-page output and multi-line texta…",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-12T05:25:29Z",
          "body_truncated": false,
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          "oid": "575a052f22053f6fcd4909d8ea31a1baf126b631",
          "body": "* Add Mitorsaw\n\n* changelog",
          "is_bot": false,
          "headline": "Add mitorsaw (#6393)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-11T13:56:48Z",
          "body_truncated": false,
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        {
          "oid": "a91105fc1c44c4edf8ad93ce1bb8c65f09428864",
          "body": "* Fix editing ACMG comments on reclassify\n\n* Remove extra space at the beginning of the comment\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix editing ACMG comments on reclassify (#6388)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-10T10:18:33Z",
          "body_truncated": false,
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        {
          "oid": "749226b3b7e40b45e3e81624ec41ddd7ae7f8b04",
          "body": "* Fix #6263 - search for specific simple id/variant id\n\n* Changelog\n\n* maybe actually keep the case query\n\n* better tooltip\n\n* fix according to test\n\n* Fix according to review\n\n* false positive...\n\n* Update scout/adapter/mongo/query.py\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* \n[…]\nrints/institutes/views.py\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* Rephrase warning slightly\n\n* and the tooltip similarly\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Search specific var (#6385)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-10T06:26:55Z",
          "body_truncated": true,
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        {
          "oid": "15806955d218a670345bd18f4b84bb81ee185f09",
          "body": "* Tooltip with LoqusDB instances description\n\n* PR ref in changelog\n\n* Simplify code\n\n* Safer code, as per review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Tooltip with LoqusDB instances description (#6384)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-09T11:27:52Z",
          "body_truncated": false,
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        },
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          "oid": "73562cd7b7eef4dbeb47b6696be3f507f8b63c71",
          "body": "* Use mock HPO terms in test\n\n* PR ref in changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Use mock HPO terms in test (#6383)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-08T08:34:21Z",
          "body_truncated": false,
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        {
          "oid": "ab9cec1cc4a8fb18fe2ac47e580b7de9cbad1031",
          "body": "* Fix #6376 - add an activate case button\n\n* Changelog\n\n* state rather than action",
          "is_bot": false,
          "headline": "Fix #6376 - add an activate case button (#6379)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-08T07:34:26Z",
          "body_truncated": false,
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        {
          "oid": "c46d38b65333f2acd31f13f7f6e22a60bdc35eb9",
          "body": "* Fix #6374 - add live search option\n\n* right, dash instead of underscore when given directly\n\n* changelog\n\n* another space\n\n* and a handful more\n\n* and another space for those\n\n* wrong type\n\n* minor formatting\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Live search (#6377)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-08T06:31:10Z",
          "body_truncated": false,
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        },
        {
          "oid": "5bff1f60f11830071db324f337000d43bb30884d",
          "body": "* Fix colspan for gene variants table - no variants found\n\n* Fix #5005 - extend filters on gene variants page\n\n* attempt to reuse secondary query builder\n\n* Fix #3946 - search SNVs and SVs CADD, gnomAD, SpliceAI, REVEL\n\n* Changelog\n\n* compact filter form: move the conceptually different OMIM genetic\n[…]\ncomment the shared / individual fields in the class for now\n\n* tooltip\n\n* see, copy-paste is hard\n\n* dash style var names in direct html\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Gene vars inheritance (#6357)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-05T14:12:36Z",
          "body_truncated": true,
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        },
        {
          "oid": "a478d4cc179d7be060f17533e3371b0e0a052fb7",
          "body": "* Add 'Has methylation' filter on cases page\n\n* Typo\n\n* Add a test\n\n* Persist has_methylation if case is updated\n\n* Thanks SonarQube\n\n* Updated changelog\n\n* Remove spacing at the beginning\n\n* Rename style and be done with it\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Add 'Has methylation' filter on cases page (#6375)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-05T13:35:42Z",
          "body_truncated": false,
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        },
        {
          "oid": "aee705675cd425efea3309c9954cb3d5edbe092e",
          "body": "* Methylation badge on cases page\n\n* Update CHANGELOG.md\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Methylation badge on cases page (#6373)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-05T11:21:23Z",
          "body_truncated": false,
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        },
        {
          "oid": "b29cfe72fde45020ffce5868bd57e8281419244c",
          "body": "* Fix #6295 - filter dark regions/sma page for gene panels\n\n* Add a Clinical HPO Dark link button to the case page\n\n* Move filter, title style\n\n* adjust title\n\n* Format dark panels filter like variants filter collapse\n\n* reorder cards\n\n* formatting\n\n* light mode reset visibility\n\n* reuse part of fun\n[…]\nof tests\n\n* revert import\n\n* Test comments\n\n* Apply suggestion from @northwestwitch\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6295 - filter dark regions/sma page for gene panels (#6353)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-05T08:42:21Z",
          "body_truncated": true,
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        },
        {
          "oid": "2871816c593600431b8b0703b793aafd95f3d1fb",
          "body": "* Only admins can edit collaborators to share cases with\n\n* Fix field reset by non-admin user\n\n* typo\n\n* common function for string values\n\n* Rename the other function\n\n* Nope, like this\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Only admins can edit collaborators to share cases with (#6370)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-04T12:45:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ed491678467eefe1b8de48de9a8e99cf5b3e723c",
          "body": "…to db (#6369)\n\n* send on ccv modifiers to post to db function\n\n* Update changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fixes bug where CCV classification ignores modifiers when submitting …",
          "author_name": "molucorner",
          "author_login": "molucorner",
          "committed_at": "2026-06-04T06:56:11Z",
          "body_truncated": false,
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        },
        {
          "oid": "539d41be895400cce8f2c722cbbb404b357bb8fc",
          "body": "* Enable link to previous ACMG classifications for SV variants\n\n* Simplify\n\n* Add PR ref to changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix SV ACMG links for previous classifications (#6365)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-03T13:51:00Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7412a9862027e01843cf779505dd4ff798ae64af",
          "body": "* Filter variants by gene OMIM disease inheritance\n\n* Forgot changelog\n\n* Add tests\n\n* Better label\n\n* Fix second col style\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Filter variants by gene OMIM disease inheritance (#6355)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-06-02T05:44:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "22397b0f3bea43b2d85542606fd3777d8354c823",
          "body": "* litvar2 links to dbsnp id\n\n* fix changelog\n\n* Display simple deep links for litvar2 on all snp ids\n\n* One is enough\n\n* js script to check for litvar availability\n\n* move variant scripts to components\n\n* no, that hits cors. make a view, and do keep the link on failure to look up\n\n* a bit more docst\n[…]\nad risky for the reward\n\n* break out subfunctions to lower complexity, change a couple of linter style suggestions\n\n* use for-of instead\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Litvar links (#6351)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-06-01T14:23:32Z",
          "body_truncated": true,
          "is_coding_agent": false
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        {
          "oid": "fd371648ea7ee9b58ea9e06d2c5176bf9d7a9daf",
          "body": "* Cache per-case genomic info when loading variants\n\n* PR ref in changelog\n\n* No need to cache genes\n\n* Clear case case and persist build-dependent info across cases, as per review\n\n* Actually clear the case cache\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Cache per-case genomic info when loading variants (#6350)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-29T08:58:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ee242092bf568b5a5c5523c6108fbc0676a045a3",
          "body": "* Work in progress\n\n* New service + tests\n\n* Fix alignment controller and relative tests\n\n* Fixed also align views\n\n* Updated changelog\n\n* Fix import\n\n* some fixed\n\n* Replace with empty string\n\n* Fix other test\n\n* Thanks SonarQube\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Replace Ensembl liftover with Broad API liftover (#6293)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-28T09:53:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4f9a994876f51a0bc2256ca3f1eb7d2512dc47dd",
          "body": "* Minor release 4.112\n\n* small fix in changelog\n\n* Fixed changelog\n\n* Fixed changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Minor release 4.112 (#6323)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-27T06:53:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "265bcff1e46a7ffe4af21f0a65885efc7b4eff2e",
          "body": "* Fix #6321 - foldable matching variants on variant page\n\n* CHANGELOG\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6321 - foldable matching variants on variant page (#6346)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-27T06:15:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "53bf34943bc48d8d010501713aec6dda9d3b6cc2",
          "body": "* Fix other warnings when loading regions and genes 38\n\n* Fix some more\n\n* final touch\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix other warnings when loading regions and genes 38 (#6348)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-27T05:41:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "90354cbd161c01ef4741133e4f0ac083dc80cd92",
          "body": "* Fix time limit in export causatives CLI\n\n* Fix PR ref in changelog\n\n* Trigger tests\n\n* Trigger tests\n\n* Retrigger tests\n\n* reretrigger tests\n\n* tests again\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Fix time limit in export causatives CLI (#6338)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-26T13:16:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c37c8fd097c747feba11e0415a46a86e342787ae",
          "body": "* Fix searching variants by gene with build 38 genes\n\n* Simplify\n\n* Safer code\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Fix search variants by gene with 38-only genes (#6340)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-26T11:01:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "48818448fb0ccd1b9ee2dde72a778172aceef40e",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6342 - load region check chromosome prefix (#6343)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-26T09:46:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b1fbe2dd289827f98eb453de4b4169b46131439e",
          "body": "* Remember search options on panel filters\n\n* Work in progress\n\n* Some more improvements\n\n* Remembers filters on panel update\n\n* Updated changelog\n\n* Use constant and update changelog\n\n* Simplify panels function\n\n* Attempt at simplifying the function\n\n* Import types\n\n* Tiny fixes\n\n* Simplify some mo\n[…]\n institute select\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>",
          "is_bot": false,
          "headline": "Remember panels filters when editing panels (#6305)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-26T05:27:57Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "19d77ca4dc8dcdce7937a4603bf2caa8861ef18c",
          "body": "…(#6312)\n\n* Improve causatives page performance by removing duplicate case queries\n\n* PR ref in changelog\n\n* Consider limit genes\n\n* Add case tags to projection for good measure\n\n* Display case status tag on causatives and verified pages\n\n* Fix merge conflict, hopefully\n\n* Nope, but not it should wo\n[…]\n\n\n* order alphabetically list and add build\n\n* Function returns an iterable\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Improve causatives page performance by removing duplicate case query …",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-25T06:23:08Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "51b3f8205cfc4b0a251ee2400db47217676615db",
          "body": "* Remove unused imports on commands export variants module\n\n* fix changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Remove unused imports on commands/export/variants module (#6334)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-25T05:27:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e36652c0f93e24a08d97c745ada9d19586e8dd18",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6332 - add mitosalt SV tag (#6333)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-22T16:04:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "dc3f8944badc16f84dad93da9f3afa3759847318",
          "body": "* Expand export causatives cli to export as managed infile\n\n* Doesn't work yet\n\n* I'm stuck\n\n* Looks like it's working\n\n* Removed unused line\n\n* Fix code style issues with Black\n\n* trigger tests\n\n* Updated changelog\n\n* Fixed, almost\n\n* wip\n\n* Fix code here and there and test\n\n* Fix restrict query by\n[…]\nent as per review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "CLI export causatives as managed (#6290)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T09:25:14Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "35065f67b3c1a72abfa312474ed97615fc2e6de8",
          "body": "* Do not default to build 37 when loading variants from a case\n\n* Fix changelog\n\n* typo\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Do not default to build 37 when loading variants from a case (#6331)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T08:56:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "688b22e4c5b34a0ef0a4bcc25654246bfa1e14c6",
          "body": "* Clearer logs with case ID when variants loading fails\n\n* PR ref\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Clearer logs with case ID when variants loading fails (#6329)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T08:34:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5a4727247ec6acb606d2fae107f0b9f95c2dc5a7",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6326 - display pending panel change comments (#6327)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-22T08:16:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4f8a199c618c5947e957aa0469e6301e10b43d3a",
          "body": "…315)\n\n* Display matching causatives' case status and tags on variant page\n\n* Add some spacing\n\n* PR ref on changelog\n\n* Better spacing\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Display matching causatives' case status and tags on variant page (#6…",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T05:57:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "591d14eef28c529d44498564e205c87f608ec298",
          "body": "… ACMG (#6325)\n\n* fix bug where likely beign overwrites benign as classification for ACMG\n\n* update changelog",
          "is_bot": false,
          "headline": "Fixes bug where likely benign overwrites benign as classification for…",
          "author_name": "molucorner",
          "author_login": "molucorner",
          "committed_at": "2026-05-22T05:39:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec9aae80ec3ff266ab7dcdf151e93c05a47e8bef",
          "body": "* Fix #6307 - add export category tags\n\n* type hints\n\n* header\n\n* unused import\n\n* CAUSATIVE is better, right\n\n* changelog...",
          "is_bot": false,
          "headline": "Fix #6307 - add export category tags (#6324)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-21T14:12:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d8ff563272f6f91ec161a514d0cfa677ddb2eae3",
          "body": "* Fix trying to load research in build 37 for cases with build 38\n\n* tiny fix\n\n* Add PR reference\n\n* Fix test accordingly\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix trying to load research in build 37 for cases with build 38 (#6322)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-21T12:58:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ba9b6eecfd311a51ff7911c81a29e273d73dbae6",
          "body": "* Add contigs on exported VCF files - managed and causatives\n\n* forgot changelog\n\n* Update scout/constants/variants_export.py\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Use different chrom size according to build\n\n* Remove comment\n\n* Added 2 new lines in VCF (source) and cli, according tp review\n\n* Add missing import\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Add contigs on exported VCF files - managed and causatives (#6310)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-21T08:51:19Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4bb63239033db832b945d54ffe268e668f2edea7",
          "body": "* Do not capitalize Paraphase region names\n\n* Also do the sorting right\n\n* Leave status as it was, as it's mostly gene names\n\n* Apply suggestion from @dnil\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Update scout/server/blueprints/cases/templates/cases/case_sma_dark.html\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Do not capitalize Paraphase region names (#6301)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T08:43:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "04756caa11732725830eddc80f3986ef6bf71a41",
          "body": "* Fix adding one managed variant in build 38\n\n* Remove typo\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix adding one managed variant in build 38 (#6300)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T05:47:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7ca2c4d278dec254d65b6ac31b6d7025aa216c1a",
          "body": "Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Display build in managed variants page (#6297)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T05:25:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "421dedc8df186613a7a2c8ced2b844abc7f94328",
          "body": "* Fix #6291 - compress demo case fusion vcf\n\n* and add the files\n\n* change filename in tests\n\n* Update changelog\n\n* Update changelog",
          "is_bot": false,
          "headline": "Fix #6291 - compress demo case fusion vcf (#6292)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-15T10:37:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e76928c195b7a84eb4ee39513eba3c05332b1e3a",
          "body": "* Version 4.111.3 - reintroduce alias for panel\n\n* and 38 fallback",
          "is_bot": false,
          "headline": "Version 4.111.3 - reintroduce alias for panel (#6289)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T17:10:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "67ff628bf08be63f93addc1439d1e687abce81be",
          "body": "…… (#6288)\n\n* Fix #6287 - partly revert aliasing, use GRCh38 to mean add chr prefix also for export variants\n\n* add help text\n\n* Prefix for export transcripts as well\n\n* Changelog\n\n* use f string\n\n* add to docs as well\n\n* citations\n\n* Ahem",
          "is_bot": false,
          "headline": "Fix #6287 - partly revert aliasing, use GRCh38 to mean add chr prefix…",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T15:13:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1c2acc5b661e0b4b09b4881409e46b23af371933",
          "body": null,
          "is_bot": false,
          "headline": "Version 4.111.1 (#6285)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T12:08:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "159651021368fdad14795996abe3cb749d4f6a86",
          "body": "* Fix #6282 - build aliases for export commands\n\n* Build for MT/M shift as well\n\n* fix test accordingly\n\n* unused imports",
          "is_bot": false,
          "headline": "Fix #6282 - build aliases for export commands (#6283)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T11:35:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "303a47ce37c367d56516939b0c5ba4da1e43b79f",
          "body": "* Version 4.111.0 release candidate\n\n* Changelog\n\n* Fixed changelog\n\n* Upgrade uv.lock to include latest chanjo and chanjo-report\n\n* update chanjo-report to 4.12.2\n\n* fresh uv.lock\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Version 4.111.0 release candidate (#6264)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T14:31:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "55e6691b6643692779b029bb23b762952119cd37",
          "body": "* Fix #6276 - CLI mito report to use both M and MT\n\n* Might as well push the chanjo-report version to latest\n\n* right\n\n* Fix #6278 - describe MT var loading in admin docs\n\n* docs\n\n* ahem, that is passed to build_query",
          "is_bot": false,
          "headline": "Fix #6276 - CLI mito report to use both M and MT (#6277)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T14:05:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a3be8242dfcb504766266e76a86d79a795fe6d66",
          "body": "* Fix #6274 - institute settings loqusdb cleared for non-admin\n\n* add tests and more getters\n\n* en passant types and html fixes\n\n* update docstring\n\n* Show all cases, show all vars are apparently user land\n\n* Update CHANGELOG.md\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* update comments\n\n* test comments\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6274 - institute settings loqusdb cleared for non-admin (#6275)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T06:18:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "90e564fc5f6fac56eee21870570d1706b54ff534",
          "body": "…t and typos (#6270)\n\n* Old expected_coverage option removed from docs, blog post, some layout and typos\n\n* Fix #6266 - Update docs on case config custom images (#6267)\n\n* changelog\n\n* like this perhaps\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Old expected_coverage option removed from docs, blog post, some layou…",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-07T12:20:46Z",
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                "key": "owner_reach",
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                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "30 out of 30 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 29/30 approved changesets -- score normalized to 9",
                "points": 6.8,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 15 contributing companies or organizations",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no dangerous workflow patterns detected",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "30 commit(s) and 27 issue activity found in the last 90 days -- score normalized to 10",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow detected",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is run on all commits",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file detected",
                "points": 2,
                "status": "partial",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "1 existing vulnerabilities detected",
                "points": 6.8,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "moderate",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories. Remaining weights renormalized. Matched 118 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 118
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 69,
            "inputs": {
              "source": "osv",
              "advisories": 2,
              "affected_packages": 1,
              "assessed_packages": 118,
              "unassessed_packages": 0,
              "affected_by_severity": "high 1",
              "direct_affected_packages": 1
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "1 affected: pdfkit 1.0.0 (high 8.4)",
                "points": 11.5,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_affected",
                    "params": {
                      "count": 1,
                      "packages": "pdfkit 1.0.0 (high 8.4)"
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory has been public longer than 90 days",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "advisories_none_stale",
                    "params": {
                      "days": 90
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 118,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
            },
            "components": [
              {
                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 11
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "moderate",
        "name": "AI Readiness",
        "value": 53,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "at_risk",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 1,
              "agent_instruction_files": [],
              "agent_instruction_max_bytes": null
            },
            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "no CLAUDE.md / AGENTS.md / editor rules",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_instructions",
                    "params": {}
                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "100 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 100,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "moderate",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 61,
            "inputs": {
              "has_nix": false,
              "has_tests": true,
              "lockfiles": [
                "uv.lock"
              ],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [
                "Makefile"
              ],
              "has_devcontainer": false,
              "has_linter_config": true,
              "typecheck_configs": [],
              "agent_commit_share": 0,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "Makefile",
                "points": 18,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Makefile"
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 22,
                "status": "met",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 11,
                "status": "met",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "Dockerfile, lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile, lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no agent-authored commits among the last 100",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_authored_commits",
                    "params": {
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
              "primary_language": "HTML",
              "largest_source_bytes": 79453,
              "source_files_sampled": 566,
              "oversized_source_files": 3
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "HTML without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "HTML"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "3/566 source files over 60KB",
                "points": 54.7,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 566,
                      "oversized": 3
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "deps.dev does not index pypi:scout-browser@4.113.3; advisories assessed against the repository dependency graph instead"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-21T20:45:21.884918Z",
  "schema_version": "0.23.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/Clinical-Genomics/scout.svg",
  "full_name": "Clinical-Genomics/scout",
  "license_state": "standard",
  "license_spdx": "BSD-3-Clause"
}