CompOmics / ms2rescore

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 7 днів.

Повний розв'язаний набір залежностей із графа залежностей GitHub: 19 прямих і 191 непрямих (транзитивних) пакетів. Транзитивне замикання є повним, коли в репозиторії закомічено lockfile.

Встановлення pypi:ms2rescore@4.0.1 тягне 69 пакетів, прямих і транзитивних: 0 мають відомі сповіщення, з них 0 — прямі залежності.

Жодне відоме сповіщення не стосується оцінених залежностей.

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.

{
  "data": {
    "repo": {
      "topics": [
        "proteomics",
        "ms2pip",
        "percolator",
        "deeplc",
        "peptide-identification"
      ],
      "is_fork": false,
      "size_kb": 326119,
      "has_wiki": false,
      "homepage": "https://ms2rescore.readthedocs.io",
      "languages": {
        "HTML": 8903,
        "Python": 337807,
        "Dockerfile": 1302,
        "Inno Setup": 1259
      },
      "pushed_at": "2026-07-24T21:35:06Z",
      "created_at": "2017-08-31T08:28:17Z",
      "owner_type": "Organization",
      "updated_at": "2026-07-24T21:20:45Z",
      "description": "Modular and user-friendly platform for AI-assisted rescoring of peptide identifications",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "Apache-2.0",
      "default_branch": "main",
      "license_spdx_raw": "Apache-2.0",
      "primary_language": "Python",
      "significant_languages": [
        "Python"
      ]
    },
    "owner": {
      "blog": "https://www.compomics.com/",
      "name": "Computational Omics and Systems Biology Group",
      "type": "Organization",
      "login": "CompOmics",
      "company": null,
      "location": "Belgium",
      "followers": 129,
      "avatar_url": "https://avatars.githubusercontent.com/u/11630937?v=4",
      "created_at": "2015-03-24T13:14:30Z",
      "is_verified": null,
      "public_repos": 114,
      "account_age_days": 4143
    },
    "license": {
      "state": "standard",
      "spdx_id": "Apache-2.0",
      "raw_spdx": "Apache-2.0",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [
        {
          "tag": "v4.0.1",
          "kind": "patch",
          "published_at": "2026-07-24T21:35:06Z"
        },
        {
          "tag": "v4.0.0",
          "kind": "major",
          "published_at": "2026-07-17T20:49:50Z"
        },
        {
          "tag": "v3.2.1",
          "kind": "patch",
          "published_at": "2026-02-10T14:03:42Z"
        },
        {
          "tag": "v3.2.0.post1",
          "kind": "other",
          "published_at": "2025-10-22T13:41:32Z"
        },
        {
          "tag": "v3.2.0",
          "kind": "minor",
          "published_at": "2025-10-20T12:34:37Z"
        },
        {
          "tag": "v3.1.5",
          "kind": "patch",
          "published_at": "2025-04-15T15:56:44Z"
        },
        {
          "tag": "v3.1.4",
          "kind": "patch",
          "published_at": "2024-12-04T16:42:43Z"
        },
        {
          "tag": "v3.1.3",
          "kind": "patch",
          "published_at": "2024-10-02T08:59:23Z"
        },
        {
          "tag": "v3.1.2",
          "kind": "patch",
          "published_at": "2024-09-18T07:16:27Z"
        },
        {
          "tag": "v3.1.1",
          "kind": "patch",
          "published_at": "2024-08-14T09:46:44Z"
        },
        {
          "tag": "v3.1.0",
          "kind": "minor",
          "published_at": "2024-07-21T18:54:55Z"
        },
        {
          "tag": "v3.1.0-dev9",
          "kind": "prerelease",
          "published_at": "2024-07-09T13:43:39Z"
        },
        {
          "tag": "v3.1.0-dev8",
          "kind": "prerelease",
          "published_at": "2024-07-08T13:26:07Z"
        },
        {
          "tag": "3.1.0-dev7",
          "kind": "prerelease",
          "published_at": "2024-07-04T17:31:06Z"
        },
        {
          "tag": "v3.1.0-dev6",
          "kind": "prerelease",
          "published_at": "2024-04-25T11:51:14Z"
        },
        {
          "tag": "v3.1.0-dev5",
          "kind": "prerelease",
          "published_at": "2024-04-18T09:21:49Z"
        },
        {
          "tag": "v3.1.0-dev4",
          "kind": "prerelease",
          "published_at": "2024-04-17T15:40:21Z"
        },
        {
          "tag": "v3.1.0-dev3",
          "kind": "prerelease",
          "published_at": "2024-04-17T15:16:37Z"
        },
        {
          "tag": "v3.1.0-dev2",
          "kind": "prerelease",
          "published_at": "2024-04-10T13:41:48Z"
        },
        {
          "tag": "v3.1.0-dev1",
          "kind": "prerelease",
          "published_at": "2024-04-09T13:22:27Z"
        },
        {
          "tag": "v3.0.3",
          "kind": "patch",
          "published_at": "2024-04-08T15:45:08Z"
        },
        {
          "tag": "v3.0.2",
          "kind": "patch",
          "published_at": "2024-03-15T12:11:50Z"
        },
        {
          "tag": "v3.0.1",
          "kind": "patch",
          "published_at": "2024-02-22T12:07:16Z"
        },
        {
          "tag": "v3.0.0",
          "kind": "major",
          "published_at": "2023-11-30T12:09:37Z"
        },
        {
          "tag": "v3.0.0-b5",
          "kind": "prerelease",
          "published_at": "2023-11-01T19:42:32Z"
        },
        {
          "tag": "v3.0.0b4",
          "kind": "other",
          "published_at": "2023-10-13T15:21:17Z"
        },
        {
          "tag": "v3.0.0-b3",
          "kind": "prerelease",
          "published_at": "2023-10-13T10:05:25Z"
        },
        {
          "tag": "3.0.0b2",
          "kind": "other",
          "published_at": "2023-10-13T08:56:35Z"
        },
        {
          "tag": "v3.0.0-b1",
          "kind": "prerelease",
          "published_at": "2023-10-12T15:57:04Z"
        },
        {
          "tag": "v3.0.0-dev4",
          "kind": "prerelease",
          "published_at": "2023-08-16T15:53:04Z"
        },
        {
          "tag": "v3.0.0-dev3",
          "kind": "prerelease",
          "published_at": "2023-06-29T18:22:02Z"
        },
        {
          "tag": "v3.0.0-dev2",
          "kind": "prerelease",
          "published_at": "2023-06-29T16:22:32Z"
        },
        {
          "tag": "v3.0.0-dev1",
          "kind": "prerelease",
          "published_at": "2023-06-29T15:35:07Z"
        },
        {
          "tag": "v2.1.3",
          "kind": "patch",
          "published_at": "2022-08-30T12:11:39Z"
        },
        {
          "tag": "v2.1.2",
          "kind": "patch",
          "published_at": "2022-04-19T12:40:33Z"
        },
        {
          "tag": "v2.1.1",
          "kind": "patch",
          "published_at": "2022-03-04T10:24:57Z"
        },
        {
          "tag": "v2.1.0",
          "kind": "minor",
          "published_at": "2021-12-14T15:17:48Z"
        },
        {
          "tag": "v2.0.0",
          "kind": "major",
          "published_at": "2021-11-21T21:18:38Z"
        },
        {
          "tag": "v2.0.0-beta.5",
          "kind": "prerelease",
          "published_at": "2021-03-04T20:15:31Z"
        },
        {
          "tag": "v2.0.0-beta.4",
          "kind": "prerelease",
          "published_at": "2021-02-15T12:56:42Z"
        },
        {
          "tag": "v2.0.0-beta.3",
          "kind": "prerelease",
          "published_at": "2021-02-10T10:19:01Z"
        },
        {
          "tag": "v2.0.0-beta.2",
          "kind": "prerelease",
          "published_at": "2021-01-26T23:43:21Z"
        },
        {
          "tag": "v0.2.2",
          "kind": "patch",
          "published_at": "2020-06-12T09:44:46Z"
        }
      ],
      "recent_commits": [
        {
          "oid": "7d2abba92aa99742be475a11fb9de8a81c621bdb",
          "body": "Resolve ruff linting errors",
          "is_bot": false,
          "headline": "Merge pull request #277 from CompOmics/fix/ruff-errors",
          "author_name": "Ralf Gabriels",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T21:20:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e4ae8dce49545722a37fdabcffa93de7b4c27a3b",
          "body": "Address BLE001, SIM115, B006, TRY004, and LOG015 findings: switch\nblind excepts to logger.exception where traceback logging is useful,\nadd noqa with rationale for genuinely intentional broad catches,\nreplace mutable default arguments, use a module logger instead of\nthe root logger, and use context managers for file opens where the\nhandle doesn't need to outlive the block.\n\nCo-authored-by: Copilot <copilot@github.com>",
          "is_bot": false,
          "headline": "fix: resolve remaining ruff lint errors in package and tests",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T21:20:09Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "d7b46a15e62ac204dc1fb9984afa2763eff5902e",
          "body": null,
          "is_bot": false,
          "headline": "chore: fix ruff linting errors without behavior changes",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T20:49:44Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1fde7b8ba4a00574e1c452965c16c607948c89c0",
          "body": null,
          "is_bot": false,
          "headline": "chore: fix automatically fixable ruff linting errors",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T20:47:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "73fc94dd678aaad193b4c1c003bd1d792bdd080f",
          "body": "Various fixes and improvements for v4.0.1",
          "is_bot": false,
          "headline": "Merge pull request #276 from CompOmics/fix/config-defaults-4.0.1",
          "author_name": "Ralf Gabriels",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T17:00:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d470e730893d820a4508f21c1906f08d5db6c1f0",
          "body": "`feature_weights_by_generator()` called `.median()` without `numeric_only=True`\non a DataFrame that still had an object-dtype `fold` column from the earlier\nmelt, raising `agg function failed [how->median,dtype->object]`. The exception\nwas caught and only logged as a warning, so the \"Feature usage in rescoring\nmodel\" section silently disappeared from every report generated since the\nristretto migration. Add `numeric_only=True`, matching the sibling\n`feature_weights()` function two lines up.",
          "is_bot": false,
          "headline": "fix(report): show missing feature-weights chart in HTML report",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T16:27:58Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "651c7b0ea68f10b3d138ebf229c734c43eb1ceb6",
          "body": null,
          "is_bot": false,
          "headline": "chore: prepare for release; bump version; update changelog",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T16:11:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "03ddf4a460f948ba6c30f5cfd3bc01951e6b4442",
          "body": null,
          "is_bot": false,
          "headline": "deps(lock): upgrade all locked dependencies",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T16:10:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3ba643f22b1f48dcdd30e3e14ded36d5cc7fe10e",
          "body": "Drop `==` pins for installer-group packages already constrained by main\ndependencies (deeplc, im2deep, ms2rescore-rs, psm_utils) -- uv.lock is a\nsingle shared resolution, so pinning them twice was redundant and only\nrisked silent drift between the two. Add `--locked` to both installer\nCI jobs so `uv\n[…]\ndency\nversions can be explicitly upgraded by running\n`uv sync --all-extras --all-groups --upgrade`\n\nAlso bump ghaction-chocolatey to v4 in both workflows.\n\nCo-authored-by: Copilot <copilot@github.com>",
          "is_bot": false,
          "headline": "build(deps): rely on uv.lock for installer versions, harden CI sync",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T16:08:37Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "e7b4faf28fa2a92987cb6ed14a3e6c7b0d27f795",
          "body": null,
          "is_bot": false,
          "headline": "docs: add more details to contribution guide",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:47:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9132c32727c18e49bd7f777e4843dc49da8575cc",
          "body": null,
          "is_bot": false,
          "headline": "chore(deps): bump deeplc to stable 4.0.0",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:42:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c8d8f68f367bf8c68f8629f7c7501d08d7580d83",
          "body": null,
          "is_bot": false,
          "headline": "docs: add computational performance section to migration guide",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:39:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6ab0c3368cd359e8b45464d3406f0a8d6c8da8fa",
          "body": "… fix/config-defaults-4.0.1\n\n# Conflicts:\n#\tCHANGELOG.md",
          "is_bot": false,
          "headline": "Merge remote-tracking branch 'origin/worktree-changelog-history' into…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:17:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3b2298f01f5004ec920db5a7bd6c69c19494cc49",
          "body": "Add entries for v2.0.0 through v3.2.1, compiled from GitHub release\nnotes, so the changelog covers full project history in Keep a\nChangelog format.",
          "is_bot": false,
          "headline": "docs: backfill CHANGELOG.md with past release notes",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:12:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "74259e21512035a2a7bef01158a8a842cb69b33a",
          "body": null,
          "is_bot": false,
          "headline": "docs: consolidate 4.0.0 alpha and stable release changelogs",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-24T15:02:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0a0973049bcfa727557307eb7ef89bf185ad8ca",
          "body": null,
          "is_bot": false,
          "headline": "docs: add migration guide",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T14:28:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5d932275af1f0e5124fce1c04a4f57a7fde40107",
          "body": "README.md had `[ProteomeDiscoverer](#)`, a bare `#` link with no real\ntarget. MyST resolves it to an empty cross-reference string, which is\nharmless locally (just a warning) but crashes sphinx-argparse's xref\nresolution on ReadTheDocs, failing the whole docs build. De-linked to\nplain text instead of guessing an unverified vendor URL.",
          "is_bot": false,
          "headline": "fix: remove placeholder link crashing ReadTheDocs build",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T14:12:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec448ea1a5bf8380a7b4f91ebb830c233b914a18",
          "body": null,
          "is_bot": false,
          "headline": "Update changelog",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T12:48:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f990cde731fa82940725928fc9bb2d8af7114134",
          "body": "…ad code\n\nmodel_dir was a real MS2PIPFeatureGenerator kwarg missing from the config\nschema, and im2deep's reference_dataset schema default claimed\n\"Meier_unimod.parquet\" while the actual default falls through to IM2Deep's\nown bundled reference dataset. Also removes an unused self._verbose\nleftover in im2deep.py, mirroring the one already removed from deeplc.py.",
          "is_bot": false,
          "headline": "fix: document im2deep's model_dir/reference_dataset defaults, drop de…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T12:46:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0c59fcbd666b5665a8e19ba829d224bd3832118",
          "body": "…e kwarg distribution\n\ndeeplc_retrain was redundant since it's already scoped under the deeplc\nfeature generator's own config block. Renamed to finetune; the old name is\nstill accepted for backward compatibility but now emits a DeprecationWarning\nand is mapped onto the new option, with an explicit finetune taking\nprecedence.\n\nAlso consolidated the near-duplicate predict/finetune kwarg filtering into a\nsingle helper, and dropped the unused self._verbose attribute.",
          "is_bot": false,
          "headline": "refactor: rename deeplc_retrain to finetune, clean up predict/finetun…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T12:10:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ef5a4a20445a0a1f97e0844d04371183ae16c91d",
          "body": "ms2_tolerance was removed as an MS2PIPFeatureGenerator kwarg in favor of the\ntop-level tolerance_value/tolerance_mode, but the key was left behind in\nconfig defaults, schema, docs, and the sage example.",
          "is_bot": false,
          "headline": "fix: remove stale ms2_tolerance from ms2pip config",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-22T11:11:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1f30d653f9044362e1a12b898aac1993bafed181",
          "body": "fix publish workflow for next release",
          "is_bot": false,
          "headline": "Update publish.yml",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-18T08:32:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "93e6125e084d8cd342cae05432f9195e82680951",
          "body": null,
          "is_bot": false,
          "headline": "updated changelog and lock file",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-17T20:38:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1fa7aedd6b7eae834a41789fbd225a686513d182",
          "body": "Release/4.0",
          "is_bot": false,
          "headline": "Merge pull request #265 from CompOmics/release/4.0",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-17T17:12:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "85906abe55c434f14015caa00436e2fbbcb65710",
          "body": null,
          "is_bot": false,
          "headline": "fix in reference dataset function im2deep",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-17T16:45:09Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1e3f5ab2f713a97d272a7f02a16749b7167f344e",
          "body": null,
          "is_bot": false,
          "headline": "code review final bugfixes and discrepancies",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-17T16:26:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "96eeeed076878e72273326cbdb1a240217db93f6",
          "body": "Fix /docs after ristretto integration",
          "is_bot": false,
          "headline": "Merge pull request #270 from CompOmics/fix/docs-after-ristretto",
          "author_name": "Ralf Gabriels",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T15:15:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ce23c8583bb8d235329e1a63f5ae4b8a3531ab18",
          "body": "… into fix/docs-after-ristretto",
          "is_bot": false,
          "headline": "Merge branch 'release/4.0' of https://github.com/CompOmics/ms2rescore…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T15:08:00Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ee8a1c83f5db86e7f7e977546b6569c2c3175707",
          "body": "Move package-level private rescoring functions to new module _ristretto_utils.py",
          "is_bot": false,
          "headline": "Merge pull request #269 from CompOmics/fix/rescoring-module",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-17T14:51:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "58f3c47bab9207a942233b5eadf5d550d75ecbe4",
          "body": null,
          "is_bot": false,
          "headline": "fix: correct test import",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T14:37:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ac1e427e50717701b80bd3a662a3acf789a487f4",
          "body": null,
          "is_bot": false,
          "headline": "docs: add rescoring module",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:57:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0f1f5231272cc9de4003dca08104a053af2814c9",
          "body": "…s2rescore into fix/docs-after-ristretto",
          "is_bot": false,
          "headline": "Merge branch 'fix/rescoring-module' of https://github.com/CompOmics/m…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:54:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e09fb2137af2ec341d131b98b317e2f5204cbc26",
          "body": null,
          "is_bot": false,
          "headline": "fix: update tests",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:52:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "adeb0ec94e5761aa92f9fb73f054eab2f4f61bc1",
          "body": null,
          "is_bot": false,
          "headline": "Move back some functions only used in rescoring.py",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:47:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bcd475395ae8cc3e41c00a3336bb450cd5adbddd",
          "body": "… into fix/rescoring-module",
          "is_bot": false,
          "headline": "Merge branch 'release/4.0' of https://github.com/CompOmics/ms2rescore…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:39:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7a52505fbf5d000501632f8e54153751a30aaa83",
          "body": "…to_utils.py",
          "is_bot": false,
          "headline": "Move package-level private rescoring functions to new module _ristret…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T13:39:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "45c45ae90c959631c34a17b0a5a73c997f10d302",
          "body": null,
          "is_bot": false,
          "headline": "end to end test",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-17T10:57:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "24fadb75b22e88d41258b33d973fe6524f07bc61",
          "body": null,
          "is_bot": false,
          "headline": "docs: update in-depth-python-api and userguide",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-17T10:23:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0ab30b69551e98415c44dc7ed42af0991ad3719e",
          "body": "Replace mokapot rescoring engine with ristretto",
          "is_bot": false,
          "headline": "Merge pull request #268 from CompOmics/feat/add-ristretto",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-17T09:03:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c255a3fcfd7fa6f8f0d4e05509e7dceba0ac7fdc",
          "body": null,
          "is_bot": false,
          "headline": "fix import error for python 3.12",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-17T08:40:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "59de3f31e2cda5fc086e12d11048967cb955805c",
          "body": "Review findings from the cumulative-diff review, addressed:\n\n- rescoring: null never actually disabled rescoring (CascadeConfig's\n  none_overrides_value=False silently ignores it), and the \"skip\n  rescoring\" path that was reachable only in principle would have\n  written no output at all. Rather than\n[…]\nreference).\n\nAlso reformats CHANGELOG.md's \"Breaking changes\" section (non-standard\nKeep a Changelog category) into the canonical Added/Changed/Removed\nsections, with breaking items tagged [BREAKING].",
          "is_bot": false,
          "headline": "Remove ability to skip rescoring; run infer_score_direction per-run",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T16:18:24Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "0f24e598a48cca9c51664b8af7140fcdd1e5711f",
          "body": "Cumulative summary of the mokapot -> ristretto rescoring engine\nmigration (report_fdr, model choice, auto score-direction inference,\noutput-file renames, GUI log.html fix, and the resulting config/API\nremovals), merged into the existing Unreleased section.",
          "is_bot": false,
          "headline": "Add ristretto migration entries to CHANGELOG",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T15:50:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fba6411e330732d1456e1d74b3f18ec60e7bd5a1",
          "body": "…of-date",
          "is_bot": false,
          "headline": "docs: minor cleanup; temporarily remove overview figure as it is out-…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T15:34:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "95a9ee6928ed58e02447e5976d956eee0a0ea214",
          "body": "The GUI's logging setup only ever attached a plain FileHandler for\n<prefix>.log.txt -- unlike the CLI, it never used a recording Rich console\nor called save_html(), so <prefix>.log.html (documented as always written)\nwas silently never created for GUI-launched runs. Added the same\nConsole(record=Tru\n[…]\naises.\n\nAlso add an INFO-level log line when rescoring actually starts, since the\nper-fold/rollup/competition detail ristretto itself logs is moving to\nDEBUG level (fixed at the source, in ristretto).",
          "is_bot": false,
          "headline": "Fix missing HTML log file in GUI runs; log when rescoring starts",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T15:07:55Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "617cec085aabe9688be7903546a398aa21330356",
          "body": "…nal API surface\n\n- Fix rescore() always returning empty feature_weights/n_iterations: it\n  rebuilds the final result via ristretto.evaluate() (no training, so those\n  fields come back empty), discarding the real values from the earlier\n  ristretto.rescore() call. Now carried over explicitly, includ\n[…]\ne that explicit rather than presenting it as public API. Also\n  privatized build_features_dataframe and fix_constant_pep, which were\n  only ever called internally within the rescoring workflow itself.",
          "is_bot": false,
          "headline": "Fix empty feature weights, simplify output naming, and minimize inter…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T14:55:43Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "dc62a277fad5dce4ed1b70d317dd237a5f3bf71e",
          "body": "A user-provided rescoring dict (e.g. \"rescoring\": {} or {\"model\": \"lda\"})\nis passed through as-is by the config cascade -- same as feature_generators\nand psm_generator, where an override is taken at face value rather than\nmerged with defaults (CascadeConfig's max_recursion_depth stops it from\nreachi\n[…]\nig[\"rescoring\"] to ristretto.rescore()\nvia **kwargs instead of naming train_fdr/model explicitly, so ristretto's\nown defaults (train_fdr=0.01, model=\"svm\") apply to whatever the user's\nconfig omitted.",
          "is_bot": false,
          "headline": "Fix KeyError on partial/empty rescoring config",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T13:10:51Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "49104a38ba6de291222a2d0afb7b84d97f3c69a5",
          "body": "Clarifies alongside the existing null (skip rescoring) note that\nrescoring: {} is equivalent to omitting the key, since cascade_config\ndeep-merges schema defaults into a partial dict. Also fixes a stale\nmention that rescoring only exposed train_fdr (model was added earlier).",
          "is_bot": false,
          "headline": "Document that an empty rescoring object uses the schema defaults",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:51:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "aa7a2c013d105819b3e32cb160a4ee28f97ea26e",
          "body": "…e-ristretto-fixes",
          "is_bot": false,
          "headline": "Merge remote-tracking branch 'origin/feat/add-ristretto' into worktre…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:50:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2610434c03c257e1a540b44e89ed151f902f327d",
          "body": "Adds a top-level report_fdr setting (default 0.01) used for console-logged\nidentification counts, HTML report stats/charts, and FlashLFQ output\nfiltering. This is independent of rescoring.train_fdr, which only controls\nristretto's semi-supervised training. Standalone report regeneration\n(ms2rescore-report) gains a --fdr option to override the report_fdr stored\nin the original run's full-config.json, without rerunning rescoring.",
          "is_bot": false,
          "headline": "Add report_fdr config option to replace hardcoded 1% FDR threshold",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:49:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8d8aec14de9bd1e2498584cf2f6425f3adc136ac",
          "body": "… into feat/add-ristretto",
          "is_bot": false,
          "headline": "Merge branch 'release/4.0' of https://github.com/CompOmics/ms2rescore…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:35:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7d8ed98782fb24870f9dd2259246c95dc9c28a3b",
          "body": "Add rescoring.model config option (svm, the default iterative\nPercolator-style SVM; or lda, a single-pass Fisher LDA that's faster\nbut less powerful on hard-to-separate datasets), threaded through to\nristretto.rescore()'s model kwarg. Adds a GUI dropdown alongside the\nexisting training-FDR field.\n\nR\n[…]\nthe jsonschema2md CLI's\npinned Python interpreter is missing on this machine (pre-existing\nenvironment issue, unrelated to this change) -- the generated\nsections were mirrored exactly by hand instead.",
          "is_bot": false,
          "headline": "Expose ristretto's model choice; always write rescoring tables",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:28:34Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "519a3bce4dadd38f3bbae60bbce0325c38d94e76",
          "body": "ristretto-ms>=0.3.0 is now on PyPI, so the local ../ironbrew editable\npath override is no longer needed. Removes the now-empty\n[tool.uv.sources] override and its TODO, and regenerates uv.lock to\nresolve ristretto-ms from the registry.",
          "is_bot": false,
          "headline": "Depend on published ristretto-ms instead of the local editable path",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T12:13:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cfe700f86ce527f199509d02908d2949192a6e55",
          "body": "Rescoring result tables are now plain TSV (not Parquet) at every\nidentification level, and only the post-rescoring (\"after\") result is\nwritten -- \"before\" is reconstructed on demand from the main PSM\nlist's provenance data, so it's never persisted. Also documents the\nmax_psm_rank_output > 1 caveat (multi-rank rows, not statistically\nrigorous FDR) and drops the now-obsolete after_report paragraph.",
          "is_bot": false,
          "headline": "Update output-files.rst for the TSV-only, after-only rescoring tables",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T11:28:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b153875ecc24fcf27c8c128467c138ad4cf65e6c",
          "body": "max_psm_rank_output is a special feature for surfacing ambiguous\nresults (e.g. mumble's multiple candidate peptidoforms per spectrum),\nnot for statistically rigorous FDR control when > 1 -- that trade-off\nis now explicit and applied consistently everywhere, instead of\ncomputing a separate always-ran\n[…]\nindexing returns the same underlying PSM\nobject references, not copies, so evaluate_before_from_provenance now\ntakes a real deep copy before mutating scores, to avoid corrupting\nthe caller's psm_list.",
          "is_bot": false,
          "headline": "Rework max_psm_rank_output and report reconstruction",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T11:27:32Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "6e425d19010c4fe6c40c969728a239c44523df98",
          "body": "build_features_dataframe now includes a \"run\" column, and every\nristretto.rescore()/evaluate() call passes run_col=\"run\" (requires\nristretto-ms>=0.3.0). Competition and CV splitting now group by\n(run, spectrum_id) at the source, instead of spectrum_id alone --\npreviously, two different physical spec\n[…]\nntirely: \"run\" now\ncomes back natively on every RescoreResult.psms from ristretto itself,\nso there's no more index-alignment hack needed on the ms2rescore side.\n\nBumps the ristretto-ms pin to >=0.3.0.",
          "is_bot": false,
          "headline": "Fix multi-run spectrum_id collisions via ristretto's new run_col",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T09:49:38Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "5a7706a3a105beba66ece6bb14458bddb7d61145",
          "body": "write_rescoring_tables() writes an additional set of *_after_report\nParquet tables when max_psm_rank_output > 1 (the rank-1 report view,\ndistinct from the multi-rank *_after files), which wasn't mentioned\nanywhere in the output-files reference.",
          "is_bot": false,
          "headline": "Document after_report Parquet output files",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T09:11:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "723a9a09d380ce588140dc97a62a400bd190202a",
          "body": "…n report\n\ncompute_id_stats/identification_overlap consumed before_result unmasked,\nunlike core.py's console-log count, which excludes mumble-generated\nalternate candidates via psm.metadata['original_psm']. Attach that\nmask onto before_result.psms itself (evaluate_before), the same way\nrun already i\n[…]\nfor that level.\n\nAdds direct unit coverage for both: _n_identified's masking behavior,\nand identification_overlap's run-based disambiguation (which the old\nbare-spectrum_id grouping would undercount).",
          "is_bot": false,
          "headline": "Apply mumble original_psm mask and run+spectrum_id key consistently i…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T09:10:35Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "96b8dc0ac4362a22dbcbb746b022ac17ce9245ee",
          "body": "fix_constant_pep previously only filtered result.psms, leaving\npeptidoform/peptide/protein rollups computed on the decoy-contaminated\npopulation -- _write_group_metadata would then look up stale\nscores/qvalues/PEPs for surviving PSMs. Now recomputes q-values, PEP,\nand rollups from scratch via ristre\n[…]\nt while the\nreal output looked fine. Split the fix into a result-only core\n(_fix_constant_pep_result) plus the existing psm_list-aware wrapper,\nand apply the core check to report_result independently.",
          "is_bot": false,
          "headline": "Refresh rollups in fix_constant_pep and apply it to report_result too",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-16T09:05:14Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "98c5d51e0dc150b5eddb4afd283f1d3f94a189d7",
          "body": null,
          "is_bot": false,
          "headline": "commit new lock file",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-16T08:13:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4726d4d10685d9d9181b5b9849d85e48ae357a0b",
          "body": "fix_constant_pep now takes/returns a (PSMList, RescoreResult) pair;\nrescore() returns (psm_list, after_result, after_report_result).\nRescoreResult.psms now always carries a run column. Adds coverage for\nthe new report_result (rank-1 view, distinct from a multi-rank final\nresult) and the after_report Parquet table written when they differ.\nAlso asserts rescoring_tables_unavailable is set when the ristretto\nParquet tables are missing.",
          "is_bot": false,
          "headline": "Update tests for rescore()'s 3-tuple return and RescoreResult schema",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T22:14:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9abf1c917111df815ddc0c3c881fb1acf1663019",
          "body": "The \"Rescoring result tables\" table had inconsistent column-divider\npositions across its border/header/content rows (four different\nwidths), which docutils/Sphinx rejects as a malformed table. Rebuilt\nit with consistent column widths (verified programmatically: every\nrow shares identical +/| column positions).",
          "is_bot": false,
          "headline": "Fix malformed RST grid table in output-files.rst",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T22:11:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f6af833dac16dc1bec5b28bc6c25b4b5aec45672",
          "body": "…p levels\n\ncreate_psm_dataframe: filter psm_list to rank==1 (the report is always\na single-best-PSM-per-spectrum view, regardless of max_psm_rank_output)\nand merge before/after by (run, spectrum_id) instead of (spectrum_id,\npeptidoform). The old peptidoform-keyed merge produced NaN\nscore_before/qval\n[…]\n after_report table (rank-1 view) over after (which may be\nmulti-rank) when both exist. The overview tab shows an explicit notice\nwhen tables are unavailable instead of silently rendering empty stats.",
          "is_bot": false,
          "headline": "Rework report before/after comparison to (run, spectrum_id) + 4 rollu…",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T22:09:00Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "27c4c4c98371b91736ed060ffb7cba8857223cf9",
          "body": "ristretto's RescoreResult schema has no room for a passthrough run\ncolumn, so attach it after the fact (index-aligned against the\noriginal PSMList) on before_result, final_result, and report_result.\nEnables merging before/after by (run, spectrum_id) in the report,\nguarding against spectrum_id collis\n[…]\nset when it differs from after (i.e. max_psm_rank_output > 1), so\nstandalone report regeneration (ms2rescore-report) can use the same\nalways-rank-1 view as a live run instead of the multi-rank result.",
          "is_bot": false,
          "headline": "Attach run to RescoreResult.psms; persist a separate after_report table",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T22:03:35Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "b6093887be54e585d636f6ca6f53b28b68e77171",
          "body": "psm.get_usi() bakes the peptidoform into the string. Once\nrename_to_usi overwrote psm_list's spectrum_id (before rescore()),\nristretto's spectrum-grouped competition -- keyed on spectrum_id --\nsaw every candidate peptidoform for a spectrum as its own singleton\ngroup, breaking competition whenever ma\n[…]\nd from psm_list).\n\nRestore the mumble-candidate exclusion (via the original_psm metadata\nflag) when counting identified PSMs before rescoring, matching what\nthe deleted _log_id_psms_before used to do.",
          "is_bot": false,
          "headline": "Fix USI/spectrum-grouping bug and always report at rank-1",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T21:44:37Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "d46c24d4acc6dd65d03edde28a5241cfbe51c503",
          "body": null,
          "is_bot": false,
          "headline": "removed local paths",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-15T16:01:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fe4573eedf3ce3de6568933c014d1431135915e1",
          "body": "_write_group_metadata crashed with KeyError for decoy PSMs whenever\nprotein-level FDR used picked-protein competition (id_decoy_pattern\nset): ristretto's picked_rollup strips the decoy pattern from group\nkeys, so strip it the same way before the lookup. Log a warning when\nplain rollup runs instead (\n[…]\nw, and correctly\ncompetes multiple candidate PSMs per spectrum (relevant since this\nruns before rank filtering). Warn when the inferred direction is\nlower-is-better, since that's the less common case.",
          "is_bot": false,
          "headline": "Fix protein rollup KeyError and improve score-direction inference",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T16:00:03Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "84cf197f5cfa4899e280ee8dc10828eb35692e17",
          "body": null,
          "is_bot": false,
          "headline": "bugfix im2deep, updated dependency packages and lockfile",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-15T15:48:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "391450bcccecccf57a809789e8847a5ad2a0ea86",
          "body": "Swap ms2rescore/rescoring_engines/mokapot.py for a new\nms2rescore/rescoring.py built on ristretto's rescore()/evaluate().\nUpdate config schema and defaults for ristretto's train_fdr, and\ndrop lower_score_is_better in favor of automatic score-direction\ninference. Rework report generation to consume ristretto's\nbefore/after RescoreResult objects. Update docs, examples, and add\nintegration tests for the new pipeline.",
          "is_bot": false,
          "headline": "Replace mokapot rescoring engine with ristretto",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-15T15:47:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b02dd3e1fda48c3f9b17ae57537baa970ee3031e",
          "body": "Mumble doc",
          "is_bot": false,
          "headline": "Merge pull request #266 from CompOmics/mumble-doc",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-15T08:25:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "108700f4e50e9c4b173576a0cbd1f4059ba08d53",
          "body": null,
          "is_bot": false,
          "headline": "updated docs accordingly",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-15T08:06:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cad73667724c01f0a93da807d08bd73d54b35515",
          "body": null,
          "is_bot": false,
          "headline": "less stringent threshold for mumble psm filtering",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-15T08:03:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ce12c6cb46a6b8533310a367c3243c3efcec669d",
          "body": "Mumble candidate PSMs are unconfirmed mass-shift hypotheses, but they\ninherit the original PSM's score/qvalue/is_decoy verbatim (mumble\nbuilds each candidate via deepcopy, only replacing the peptidoform).\nfilter_mumble_psms() only runs after the feature-generator loop, so\nDeepLC/IM2Deep's q-value-ba\n[…]\n, several same-spectrum candidates can tie on\nrescoring score; which one is kept as the top hit is not deterministic\n(pandas' default sort is not stable), only cosmetic ordering, not a\nreal tie-break.",
          "is_bot": false,
          "headline": "fix: exclude unconfirmed Mumble PSMs from RT/CCS calibration",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T15:48:21Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "37453df870a8bedfa308e11661012cad999f1f10",
          "body": "Mumble had no dedicated documentation: no user guide page, and the\nconfig schema for its \"psm_generator\" entry was incomplete and\ncontained wrong defaults/descriptions (mass_error default 0.2 instead\nof 0.02, fasta_file description copy-pasted from another option).\n\nAdd a full user guide page, a \"Co\n[…]\nmplete\nthe mumble config schema to match the real Mumble API\n(combination_length, exclude_mutations, modification_file,\nall_unimod_modifications). All surfaces explicitly mark Mumble as\nbeta software.",
          "is_bot": false,
          "headline": "docs: add Mumble PSM generator documentation, mark as beta",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T13:35:08Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "6589ba26c844f21d1da786af65dde9fc4f3e5fe6",
          "body": null,
          "is_bot": false,
          "headline": "updated pyproject and lock file",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T13:19:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "53e4cee30fabdcc690b95727598909ffd9660668",
          "body": "Percolator removal",
          "is_bot": false,
          "headline": "Merge pull request #264 from CompOmics/percolator-removal",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-14T12:18:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3b26484cdfeec22a253100d3d47961472f718a95",
          "body": "deps: remove tomli (was only required for Python <3.11)",
          "is_bot": false,
          "headline": "Merge pull request #262 from CompOmics/deps/remove-tomli",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-14T12:15:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fd0976d24079e7e87c6e04abcdbc41c218269e65",
          "body": null,
          "is_bot": false,
          "headline": "documentation update",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T12:13:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bfd8a685870dc88c118ab0d9b854a67208d6a42a",
          "body": null,
          "is_bot": false,
          "headline": "updated documentation without percolator",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T12:08:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5d197c5b48bfa71f6bf5c68e280d8a121b58e129",
          "body": null,
          "is_bot": false,
          "headline": "removed percolator",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T12:08:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2f04133d9ecd20ede300952b447eff9f6533218e",
          "body": "In memory report",
          "is_bot": false,
          "headline": "Merge pull request #263 from CompOmics/in-memory-report",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-14T11:30:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "05f3fd973ac9ce9c98d6b6038f7045904d2ed87b",
          "body": null,
          "is_bot": false,
          "headline": "updated style and template of plotting",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T11:25:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6f293d1a98d4b30692800b5a5f429db92f5aa2d7",
          "body": null,
          "is_bot": false,
          "headline": "deeplc bug fix to select best head not just first head",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T09:40:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7e592786a35ab48bcc0d5485e659b83bdc8281d9",
          "body": null,
          "is_bot": false,
          "headline": "updated lock file",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T09:11:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "01ba11c63442d40de6cb011c29442702e7dfaae9",
          "body": null,
          "is_bot": false,
          "headline": "new testcases for report",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T07:47:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "83ebcc20577bdfd92f12514a96ca975673fdf46d",
          "body": null,
          "is_bot": false,
          "headline": "changes in the api of how report is generated",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T07:47:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "45f9b33565447958bd08425fb481fd25bf089c8e",
          "body": null,
          "is_bot": false,
          "headline": "changes to report using new dataclass and helper functions",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T07:46:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0a7d49af5d1be33b0414feab4094da4fd5c9110",
          "body": null,
          "is_bot": false,
          "headline": "new dataclass for report generation",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-14T07:46:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6a4ac7352e2d59c80d9e517262c35fb1351b5cb3",
          "body": "Test suite",
          "is_bot": false,
          "headline": "Merge pull request #261 from CompOmics/test-suite",
          "author_name": "ArthurDeclercq",
          "author_login": "ArthurDeclercq",
          "committed_at": "2026-07-13T16:45:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "884b7dae76a1783d2853dc3d3bf013dc872469a4",
          "body": null,
          "is_bot": false,
          "headline": "update pyproject with new versions of im2deep, ms2pip and ms2rescore-rs",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-13T16:40:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "35b1aae43181e6a849f2ce7b597fd6b0efea700b",
          "body": null,
          "is_bot": false,
          "headline": "deps: remove tomli (was only required for Python <3.11)",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-13T16:40:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fb0a03dc84983643b404698ad8803b488bb391ad",
          "body": null,
          "is_bot": false,
          "headline": "release spectra before rescoring",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-13T16:02:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "dbe5b6fe40cec21ff5958c7ee9f13556d76bace3",
          "body": null,
          "is_bot": false,
          "headline": "small change fg to fix potential bugs",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-13T13:56:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a31739314b8f486d223652b51a3df73c2b02cbcf",
          "body": null,
          "is_bot": false,
          "headline": "removed deprecation warnings",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-13T13:56:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "787e6748338ea7158977a1379bd3a3852d9960be",
          "body": null,
          "is_bot": false,
          "headline": "add additional tests for the feature generators",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-13T13:38:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "112bec6274cc61733b87481e549afd7aaecd740b",
          "body": "…ation\n\nrefactor: Centralize spectrum annotation and migrate to new ms2pip/ms2 APIs",
          "is_bot": false,
          "headline": "Merge pull request #260 from CompOmics/feat/centralize-spectrum-annot…",
          "author_name": "Ralf Gabriels",
          "author_login": "RalfG",
          "committed_at": "2026-07-10T10:45:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5d89a11c542102d925663ce75d4dc3c47e6c1549",
          "body": null,
          "is_bot": false,
          "headline": "removed unused import",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-10T09:15:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3d7288eb80df733427cde91ff2b01b07860da3ca",
          "body": null,
          "is_bot": false,
          "headline": "ms2fg tests",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-10T08:47:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a5467969171d81ea5b97671f91661312f9b4447e",
          "body": null,
          "is_bot": false,
          "headline": "remove unused import from ms2rescore_rs",
          "author_name": "ArthurDeclercq",
          "author_login": null,
          "committed_at": "2026-07-10T08:19:23Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9d957e8f1316fcd996ec776d2df24dcf33134380",
          "body": null,
          "is_bot": false,
          "headline": "fix: unused import and overeager linter checks",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-09T11:38:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "198b05095be7c2da894a2016a37802bb1c948a01",
          "body": null,
          "is_bot": false,
          "headline": "update changelog",
          "author_name": "RalfG",
          "author_login": "RalfG",
          "committed_at": "2026-07-09T11:31:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        }
      ],
      "releases_count": 43,
      "commits_last_year": 210,
      "latest_release_at": "2026-07-24T21:35:06Z",
      "latest_release_tag": "v4.0.1",
      "releases_from_tags": false,
      "days_since_last_push": 3,
      "active_weeks_last_year": 19,
      "days_since_latest_release": 3,
      "mean_days_between_releases": 78.8
    },
    "community": {
      "has_readme": true,
      "has_license": true,
      "has_description": true,
      "has_contributing": true,
      "health_percentage": 50,
      "has_issue_template": false,
      "has_code_of_conduct": false,
      "has_pull_request_template": false
    },
    "ecosystem": {
      "packages": [
        {
          "name": "ms2rescore",
          "exists": true,
          "license": null,
          "keywords": [
            "MS2Rescore",
            "MS2PIP",
            "DeepLC",
            "proteomics",
            "mass spectrometry",
            "peptide identification",
            "rescoring",
            "machine learning",
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
          ],
          "ecosystem": "pypi",
          "matches_repo": true,
          "registry_url": "https://pypi.org/project/ms2rescore/",
          "is_deprecated": false,
          "latest_version": "4.0.1",
          "repository_url": "https://github.com/compomics/ms2rescore",
          "versions_count": 45,
          "total_downloads": null,
          "dependents_count": null,
          "deprecation_note": null,
          "maintainers_count": null,
          "monthly_downloads": null,
          "first_published_at": "2021-01-26T23:44:46.259527Z",
          "latest_published_at": "2026-07-24T21:38:07.815872Z",
          "latest_version_yanked": null,
          "days_since_latest_publish": 3
        }
      ]
    },
    "popularity": {
      "forks": 22,
      "stars": 66,
      "watchers": 6,
      "fork_history": {
        "days": [
          {
            "date": "2019-08-26",
            "count": 1
          },
          {
            "date": "2021-12-15",
            "count": 1
          },
          {
            "date": "2022-01-15",
            "count": 1
          },
          {
            "date": "2022-02-03",
            "count": 1
          },
          {
            "date": "2022-04-07",
            "count": 1
          },
          {
            "date": "2022-08-26",
            "count": 1
          },
          {
            "date": "2022-09-21",
            "count": 1
          },
          {
            "date": "2023-03-07",
            "count": 1
          },
          {
            "date": "2023-04-19",
            "count": 1
          },
          {
            "date": "2023-10-19",
            "count": 1
          },
          {
            "date": "2023-12-07",
            "count": 1
          },
          {
            "date": "2024-01-09",
            "count": 1
          },
          {
            "date": "2024-03-10",
            "count": 1
          },
          {
            "date": "2024-03-21",
            "count": 1
          },
          {
            "date": "2024-10-03",
            "count": 1
          },
          {
            "date": "2025-02-10",
            "count": 1
          },
          {
            "date": "2025-02-27",
            "count": 1
          },
          {
            "date": "2025-03-25",
            "count": 1
          },
          {
            "date": "2025-06-12",
            "count": 1
          },
          {
            "date": "2025-10-07",
            "count": 1
          },
          {
            "date": "2026-04-13",
            "count": 1
          },
          {
            "date": "2026-06-29",
            "count": 1
          }
        ],
        "complete": true,
        "collected": 22,
        "total_forks": 22
      },
      "star_history": null,
      "open_issues_and_prs": 14
    },
    "ai_readiness": {
      "has_nix": false,
      "example_dirs": [
        "examples",
        "notebooks"
      ],
      "has_llms_txt": false,
      "has_dockerfile": true,
      "has_mcp_signal": false,
      "bootstrap_files": [],
      "api_schema_files": [],
      "has_devcontainer": false,
      "typecheck_configs": [],
      "toolchain_manifests": [],
      "largest_source_bytes": 116571,
      "source_files_sampled": 49,
      "oversized_source_files": 1,
      "agent_instruction_files": [],
      "agent_instruction_max_bytes": null
    },
    "dependencies": {
      "manifests": [
        "pyproject.toml"
      ],
      "advisories": {
        "error": null,
        "scope": "published_package",
        "source": "osv",
        "findings": [],
        "collected": true,
        "malicious": [],
        "truncated": false,
        "by_severity": {},
        "advisory_count": 0,
        "affected_count": 0,
        "assessed_count": 69,
        "malicious_count": 0,
        "assessed_package": "pypi:ms2rescore@4.0.1",
        "unassessed_count": 0,
        "direct_affected_count": 0
      },
      "ecosystems": [
        "pypi"
      ],
      "dependencies": [
        {
          "name": "cascade-config",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=0.4.0"
        },
        {
          "name": "click",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=7"
        },
        {
          "name": "customtkinter",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=5,<6"
        },
        {
          "name": "deeplc",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=4.0.0"
        },
        {
          "name": "im2deep",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=2.0.1"
        },
        {
          "name": "jinja2",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=3"
        },
        {
          "name": "lxml",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=4.5"
        },
        {
          "name": "ms2pip",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=4.2.0"
        },
        {
          "name": "ms2rescore_rs",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=0.5.0"
        },
        {
          "name": "numpy",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=1.25,<3.0"
        },
        {
          "name": "packaging",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=25.0"
        },
        {
          "name": "pandas",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=1"
        },
        {
          "name": "plotly",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=5"
        },
        {
          "name": "psm_utils",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=1.1"
        },
        {
          "name": "pyarrow",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=14"
        },
        {
          "name": "pyteomics",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=4.7.2"
        },
        {
          "name": "rich",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=12"
        },
        {
          "name": "ristretto-ms",
          "manifest": "pyproject.toml",
          "ecosystem": "pypi",
          "version_constraint": ">=0.3.0"
        }
      ],
      "all_dependencies": {
        "error": null,
        "source": "github-sbom",
        "packages": [
          {
            "name": "cascade-config",
            "direct": true,
            "version": "0.4.0",
            "ecosystem": "pypi"
          },
          {
            "name": "click",
            "direct": true,
            "version": "8.4.2",
            "ecosystem": "pypi"
          },
          {
            "name": "customtkinter",
            "direct": true,
            "version": "5.2.2",
            "ecosystem": "pypi"
          },
          {
            "name": "deeplc",
            "direct": true,
            "version": "4.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "im2deep",
            "direct": true,
            "version": "2.0.2",
            "ecosystem": "pypi"
          },
          {
            "name": "jinja2",
            "direct": true,
            "version": "3.1.6",
            "ecosystem": "pypi"
          },
          {
            "name": "lxml",
            "direct": true,
            "version": "6.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "ms2pip",
            "direct": true,
            "version": "4.2.0",
            "ecosystem": "pypi"
          },
          {
            "name": "ms2rescore-rs",
            "direct": true,
            "version": "0.5.0",
            "ecosystem": "pypi"
          },
          {
            "name": "numpy",
            "direct": true,
            "version": "2.4.6",
            "ecosystem": "pypi"
          },
          {
            "name": "numpy",
            "direct": true,
            "version": "2.5.1",
            "ecosystem": "pypi"
          },
          {
            "name": "packaging",
            "direct": true,
            "version": "26.2",
            "ecosystem": "pypi"
          },
          {
            "name": "pandas",
            "direct": true,
            "version": "2.3.3",
            "ecosystem": "pypi"
          },
          {
            "name": "plotly",
            "direct": true,
            "version": "6.9.0",
            "ecosystem": "pypi"
          },
          {
            "name": "psm-utils",
            "direct": true,
            "version": "1.5.5",
            "ecosystem": "pypi"
          },
          {
            "name": "pyarrow",
            "direct": true,
            "version": "25.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pyteomics",
            "direct": true,
            "version": "4.7.5",
            "ecosystem": "pypi"
          },
          {
            "name": "rich",
            "direct": true,
            "version": "14.3.4",
            "ecosystem": "pypi"
          },
          {
            "name": "ristretto-ms",
            "direct": true,
            "version": "0.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "aiohappyeyeballs",
            "direct": false,
            "version": "2.7.1",
            "ecosystem": "pypi"
          },
          {
            "name": "aiohttp",
            "direct": false,
            "version": "3.14.3",
            "ecosystem": "pypi"
          },
          {
            "name": "aiosignal",
            "direct": false,
            "version": "1.4.0",
            "ecosystem": "pypi"
          },
          {
            "name": "alabaster",
            "direct": false,
            "version": "1.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "altgraph",
            "direct": false,
            "version": "0.17.5",
            "ecosystem": "pypi"
          },
          {
            "name": "annotated-types",
            "direct": false,
            "version": "0.8.0",
            "ecosystem": "pypi"
          },
          {
            "name": "anyio",
            "direct": false,
            "version": "4.14.2",
            "ecosystem": "pypi"
          },
          {
            "name": "appnope",
            "direct": false,
            "version": "0.1.4",
            "ecosystem": "pypi"
          },
          {
            "name": "asttokens",
            "direct": false,
            "version": "3.0.2",
            "ecosystem": "pypi"
          },
          {
            "name": "attrs",
            "direct": false,
            "version": "26.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "babel",
            "direct": false,
            "version": "2.18.0",
            "ecosystem": "pypi"
          },
          {
            "name": "beautifulsoup4",
            "direct": false,
            "version": "4.15.0",
            "ecosystem": "pypi"
          },
          {
            "name": "black",
            "direct": false,
            "version": "26.5.1",
            "ecosystem": "pypi"
          },
          {
            "name": "bleach",
            "direct": false,
            "version": "6.4.0",
            "ecosystem": "pypi"
          },
          {
            "name": "cbor2",
            "direct": false,
            "version": "6.1.3",
            "ecosystem": "pypi"
          },
          {
            "name": "certifi",
            "direct": false,
            "version": "2026.7.22",
            "ecosystem": "pypi"
          },
          {
            "name": "cffi",
            "direct": false,
            "version": "2.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "cfgv",
            "direct": false,
            "version": "3.5.0",
            "ecosystem": "pypi"
          },
          {
            "name": "charset-normalizer",
            "direct": false,
            "version": "3.4.9",
            "ecosystem": "pypi"
          },
          {
            "name": "colorama",
            "direct": false,
            "version": "0.4.6",
            "ecosystem": "pypi"
          },
          {
            "name": "comm",
            "direct": false,
            "version": "0.2.3",
            "ecosystem": "pypi"
          },
          {
            "name": "contourpy",
            "direct": false,
            "version": "1.3.3",
            "ecosystem": "pypi"
          },
          {
            "name": "coverage",
            "direct": false,
            "version": "7.15.2",
            "ecosystem": "pypi"
          },
          {
            "name": "cuda-bindings",
            "direct": false,
            "version": "13.3.1",
            "ecosystem": "pypi"
          },
          {
            "name": "cuda-pathfinder",
            "direct": false,
            "version": "1.6.0",
            "ecosystem": "pypi"
          },
          {
            "name": "cuda-toolkit",
            "direct": false,
            "version": "13.0.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "cycler",
            "direct": false,
            "version": "0.12.1",
            "ecosystem": "pypi"
          },
          {
            "name": "darkdetect",
            "direct": false,
            "version": "0.8.0",
            "ecosystem": "pypi"
          },
          {
            "name": "debugpy",
            "direct": false,
            "version": "1.8.21",
            "ecosystem": "pypi"
          },
          {
            "name": "decorator",
            "direct": false,
            "version": "5.3.1",
            "ecosystem": "pypi"
          },
          {
            "name": "defusedxml",
            "direct": false,
            "version": "0.7.1",
            "ecosystem": "pypi"
          },
          {
            "name": "distlib",
            "direct": false,
            "version": "0.4.3",
            "ecosystem": "pypi"
          },
          {
            "name": "docutils",
            "direct": false,
            "version": "0.22.4",
            "ecosystem": "pypi"
          },
          {
            "name": "executing",
            "direct": false,
            "version": "2.2.1",
            "ecosystem": "pypi"
          },
          {
            "name": "fastjsonschema",
            "direct": false,
            "version": "2.21.2",
            "ecosystem": "pypi"
          },
          {
            "name": "filelock",
            "direct": false,
            "version": "3.32.0",
            "ecosystem": "pypi"
          },
          {
            "name": "fonttools",
            "direct": false,
            "version": "4.63.0",
            "ecosystem": "pypi"
          },
          {
            "name": "frozenlist",
            "direct": false,
            "version": "1.8.0",
            "ecosystem": "pypi"
          },
          {
            "name": "fsspec",
            "direct": false,
            "version": "2026.6.0",
            "ecosystem": "pypi"
          },
          {
            "name": "greenlet",
            "direct": false,
            "version": "3.5.4",
            "ecosystem": "pypi"
          },
          {
            "name": "h11",
            "direct": false,
            "version": "0.16.0",
            "ecosystem": "pypi"
          },
          {
            "name": "identify",
            "direct": false,
            "version": "2.6.19",
            "ecosystem": "pypi"
          },
          {
            "name": "idna",
            "direct": false,
            "version": "3.18",
            "ecosystem": "pypi"
          },
          {
            "name": "imagesize",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "iniconfig",
            "direct": false,
            "version": "2.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "ipykernel",
            "direct": false,
            "version": "7.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "ipython",
            "direct": false,
            "version": "9.15.0",
            "ecosystem": "pypi"
          },
          {
            "name": "ipython-pygments-lexers",
            "direct": false,
            "version": "1.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "ipywidgets",
            "direct": false,
            "version": "8.1.8",
            "ecosystem": "pypi"
          },
          {
            "name": "jedi",
            "direct": false,
            "version": "0.20.0",
            "ecosystem": "pypi"
          },
          {
            "name": "joblib",
            "direct": false,
            "version": "1.5.3",
            "ecosystem": "pypi"
          },
          {
            "name": "jsonschema",
            "direct": false,
            "version": "4.26.0",
            "ecosystem": "pypi"
          },
          {
            "name": "jsonschema-specifications",
            "direct": false,
            "version": "2025.9.1",
            "ecosystem": "pypi"
          },
          {
            "name": "jupyter-client",
            "direct": false,
            "version": "8.9.1",
            "ecosystem": "pypi"
          },
          {
            "name": "jupyter-core",
            "direct": false,
            "version": "5.9.1",
            "ecosystem": "pypi"
          },
          {
            "name": "jupyterlab-pygments",
            "direct": false,
            "version": "0.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "jupyterlab-widgets",
            "direct": false,
            "version": "3.0.16",
            "ecosystem": "pypi"
          },
          {
            "name": "kiwisolver",
            "direct": false,
            "version": "1.5.0",
            "ecosystem": "pypi"
          },
          {
            "name": "lightning",
            "direct": false,
            "version": "2.6.5",
            "ecosystem": "pypi"
          },
          {
            "name": "lightning-utilities",
            "direct": false,
            "version": "0.15.3",
            "ecosystem": "pypi"
          },
          {
            "name": "macholib",
            "direct": false,
            "version": "1.16.4",
            "ecosystem": "pypi"
          },
          {
            "name": "markdown-it-py",
            "direct": false,
            "version": "4.2.0",
            "ecosystem": "pypi"
          },
          {
            "name": "markupsafe",
            "direct": false,
            "version": "3.0.3",
            "ecosystem": "pypi"
          },
          {
            "name": "matplotlib",
            "direct": false,
            "version": "3.11.1",
            "ecosystem": "pypi"
          },
          {
            "name": "matplotlib-inline",
            "direct": false,
            "version": "0.2.2",
            "ecosystem": "pypi"
          },
          {
            "name": "mdit-py-plugins",
            "direct": false,
            "version": "0.6.1",
            "ecosystem": "pypi"
          },
          {
            "name": "mdurl",
            "direct": false,
            "version": "0.1.2",
            "ecosystem": "pypi"
          },
          {
            "name": "mistune",
            "direct": false,
            "version": "3.3.4",
            "ecosystem": "pypi"
          },
          {
            "name": "ml-dtypes",
            "direct": false,
            "version": "0.5.4",
            "ecosystem": "pypi"
          },
          {
            "name": "mpmath",
            "direct": false,
            "version": "1.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "ms2rescore",
            "direct": false,
            "version": "4.0.1",
            "ecosystem": "pypi"
          },
          {
            "name": "multidict",
            "direct": false,
            "version": "6.7.1",
            "ecosystem": "pypi"
          },
          {
            "name": "mumble",
            "direct": false,
            "version": "0.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "mypy-extensions",
            "direct": false,
            "version": "1.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "myst-parser",
            "direct": false,
            "version": "5.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "narwhals",
            "direct": false,
            "version": "2.24.0",
            "ecosystem": "pypi"
          },
          {
            "name": "nbclient",
            "direct": false,
            "version": "0.11.0",
            "ecosystem": "pypi"
          },
          {
            "name": "nbconvert",
            "direct": false,
            "version": "7.17.1",
            "ecosystem": "pypi"
          },
          {
            "name": "nbformat",
            "direct": false,
            "version": "5.10.4",
            "ecosystem": "pypi"
          },
          {
            "name": "nbsphinx",
            "direct": false,
            "version": "0.9.8",
            "ecosystem": "pypi"
          },
          {
            "name": "nest-asyncio2",
            "direct": false,
            "version": "1.7.2",
            "ecosystem": "pypi"
          },
          {
            "name": "networkx",
            "direct": false,
            "version": "3.6.1",
            "ecosystem": "pypi"
          },
          {
            "name": "nodeenv",
            "direct": false,
            "version": "1.10.0",
            "ecosystem": "pypi"
          },
          {
            "name": "numpydoc",
            "direct": false,
            "version": "1.10.0",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cublas",
            "direct": false,
            "version": "13.1.1.3",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cuda-cupti",
            "direct": false,
            "version": "13.0.85",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cuda-nvrtc",
            "direct": false,
            "version": "13.0.88",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cuda-runtime",
            "direct": false,
            "version": "13.0.96",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cudnn-cu13",
            "direct": false,
            "version": "9.20.0.48",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cufft",
            "direct": false,
            "version": "12.0.0.61",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cufile",
            "direct": false,
            "version": "1.15.1.6",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-curand",
            "direct": false,
            "version": "10.4.0.35",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cusolver",
            "direct": false,
            "version": "12.0.4.66",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cusparse",
            "direct": false,
            "version": "12.6.3.3",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-cusparselt-cu13",
            "direct": false,
            "version": "0.8.1",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-nccl-cu12",
            "direct": false,
            "version": "2.30.7",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-nccl-cu13",
            "direct": false,
            "version": "2.29.7",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-nvjitlink",
            "direct": false,
            "version": "13.3.33",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-nvshmem-cu13",
            "direct": false,
            "version": "3.4.5",
            "ecosystem": "pypi"
          },
          {
            "name": "nvidia-nvtx",
            "direct": false,
            "version": "13.0.85",
            "ecosystem": "pypi"
          },
          {
            "name": "onnx",
            "direct": false,
            "version": "1.22.0",
            "ecosystem": "pypi"
          },
          {
            "name": "onnx2torch",
            "direct": false,
            "version": "1.5.15",
            "ecosystem": "pypi"
          },
          {
            "name": "pandocfilters",
            "direct": false,
            "version": "1.5.1",
            "ecosystem": "pypi"
          },
          {
            "name": "parso",
            "direct": false,
            "version": "0.8.7",
            "ecosystem": "pypi"
          },
          {
            "name": "pathspec",
            "direct": false,
            "version": "1.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "pefile",
            "direct": false,
            "version": "2024.8.26",
            "ecosystem": "pypi"
          },
          {
            "name": "pexpect",
            "direct": false,
            "version": "4.9.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pillow",
            "direct": false,
            "version": "12.3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "platformdirs",
            "direct": false,
            "version": "4.11.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pluggy",
            "direct": false,
            "version": "1.6.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pre-commit",
            "direct": false,
            "version": "4.6.1",
            "ecosystem": "pypi"
          },
          {
            "name": "prompt-toolkit",
            "direct": false,
            "version": "3.0.52",
            "ecosystem": "pypi"
          },
          {
            "name": "propcache",
            "direct": false,
            "version": "0.5.2",
            "ecosystem": "pypi"
          },
          {
            "name": "protobuf",
            "direct": false,
            "version": "7.35.1",
            "ecosystem": "pypi"
          },
          {
            "name": "psims",
            "direct": false,
            "version": "1.3.6",
            "ecosystem": "pypi"
          },
          {
            "name": "psutil",
            "direct": false,
            "version": "7.2.2",
            "ecosystem": "pypi"
          },
          {
            "name": "ptyprocess",
            "direct": false,
            "version": "0.7.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pure-eval",
            "direct": false,
            "version": "0.2.3",
            "ecosystem": "pypi"
          },
          {
            "name": "pycparser",
            "direct": false,
            "version": "3.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pydantic",
            "direct": false,
            "version": "2.13.4",
            "ecosystem": "pypi"
          },
          {
            "name": "pydantic-core",
            "direct": false,
            "version": "2.46.4",
            "ecosystem": "pypi"
          },
          {
            "name": "pygments",
            "direct": false,
            "version": "2.20.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pyinstaller",
            "direct": false,
            "version": "6.21.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pyinstaller-hooks-contrib",
            "direct": false,
            "version": "2026.6",
            "ecosystem": "pypi"
          },
          {
            "name": "pyopenms",
            "direct": false,
            "version": "3.5.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pyparsing",
            "direct": false,
            "version": "3.3.2",
            "ecosystem": "pypi"
          },
          {
            "name": "pytest",
            "direct": false,
            "version": "9.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "pytest-cov",
            "direct": false,
            "version": "7.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "python-dateutil",
            "direct": false,
            "version": "2.9.0.post0",
            "ecosystem": "pypi"
          },
          {
            "name": "python-discovery",
            "direct": false,
            "version": "1.5.0",
            "ecosystem": "pypi"
          },
          {
            "name": "pytokens",
            "direct": false,
            "version": "0.4.1",
            "ecosystem": "pypi"
          },
          {
            "name": "pytorch-lightning",
            "direct": false,
            "version": "2.6.5",
            "ecosystem": "pypi"
          },
          {
            "name": "pytz",
            "direct": false,
            "version": "2026.2",
            "ecosystem": "pypi"
          },
          {
            "name": "pywin32-ctypes",
            "direct": false,
            "version": "0.2.3",
            "ecosystem": "pypi"
          },
          {
            "name": "pyyaml",
            "direct": false,
            "version": "6.0.3",
            "ecosystem": "pypi"
          },
          {
            "name": "pyzmq",
            "direct": false,
            "version": "27.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "referencing",
            "direct": false,
            "version": "0.37.0",
            "ecosystem": "pypi"
          },
          {
            "name": "requests",
            "direct": false,
            "version": "2.34.2",
            "ecosystem": "pypi"
          },
          {
            "name": "roman-numerals",
            "direct": false,
            "version": "4.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "rpds-py",
            "direct": false,
            "version": "2026.6.3",
            "ecosystem": "pypi"
          },
          {
            "name": "ruff",
            "direct": false,
            "version": "0.16.0",
            "ecosystem": "pypi"
          },
          {
            "name": "rustyms",
            "direct": false,
            "version": "0.10.0",
            "ecosystem": "pypi"
          },
          {
            "name": "scikit-learn",
            "direct": false,
            "version": "1.9.0",
            "ecosystem": "pypi"
          },
          {
            "name": "scipy",
            "direct": false,
            "version": "1.17.1",
            "ecosystem": "pypi"
          },
          {
            "name": "scipy",
            "direct": false,
            "version": "1.18.0",
            "ecosystem": "pypi"
          },
          {
            "name": "semver",
            "direct": false,
            "version": "3.0.4",
            "ecosystem": "pypi"
          },
          {
            "name": "setuptools",
            "direct": false,
            "version": "83.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "six",
            "direct": false,
            "version": "1.17.0",
            "ecosystem": "pypi"
          },
          {
            "name": "snowballstemmer",
            "direct": false,
            "version": "3.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "soupsieve",
            "direct": false,
            "version": "2.9.1",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx",
            "direct": false,
            "version": "9.0.4",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx",
            "direct": false,
            "version": "9.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-argparse",
            "direct": false,
            "version": "0.6.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-autobuild",
            "direct": false,
            "version": "2025.8.25",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-inline-tabs",
            "direct": false,
            "version": "2025.12.21.14",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-rtd-theme",
            "direct": false,
            "version": "3.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-applehelp",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-devhelp",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-htmlhelp",
            "direct": false,
            "version": "2.1.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-jquery",
            "direct": false,
            "version": "4.1",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-jsmath",
            "direct": false,
            "version": "1.0.1",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-qthelp",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinxcontrib-serializinghtml",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          },
          {
            "name": "sqlalchemy",
            "direct": false,
            "version": "2.0.51",
            "ecosystem": "pypi"
          },
          {
            "name": "stack-data",
            "direct": false,
            "version": "0.6.3",
            "ecosystem": "pypi"
          },
          {
            "name": "starlette",
            "direct": false,
            "version": "1.3.1",
            "ecosystem": "pypi"
          },
          {
            "name": "sympy",
            "direct": false,
            "version": "1.14.0",
            "ecosystem": "pypi"
          },
          {
            "name": "threadpoolctl",
            "direct": false,
            "version": "3.6.0",
            "ecosystem": "pypi"
          },
          {
            "name": "tinycss2",
            "direct": false,
            "version": "1.5.1",
            "ecosystem": "pypi"
          },
          {
            "name": "tomli",
            "direct": false,
            "version": "2.4.1",
            "ecosystem": "pypi"
          },
          {
            "name": "torch",
            "direct": false,
            "version": "2.13.0",
            "ecosystem": "pypi"
          },
          {
            "name": "torchmetrics",
            "direct": false,
            "version": "1.9.0",
            "ecosystem": "pypi"
          },
          {
            "name": "torchvision",
            "direct": false,
            "version": "0.28.0",
            "ecosystem": "pypi"
          },
          {
            "name": "tornado",
            "direct": false,
            "version": "6.5.7",
            "ecosystem": "pypi"
          },
          {
            "name": "tqdm",
            "direct": false,
            "version": "4.69.1",
            "ecosystem": "pypi"
          },
          {
            "name": "traitlets",
            "direct": false,
            "version": "5.15.1",
            "ecosystem": "pypi"
          },
          {
            "name": "triton",
            "direct": false,
            "version": "3.7.1",
            "ecosystem": "pypi"
          },
          {
            "name": "typing-extensions",
            "direct": false,
            "version": "4.16.0",
            "ecosystem": "pypi"
          },
          {
            "name": "typing-inspection",
            "direct": false,
            "version": "0.4.2",
            "ecosystem": "pypi"
          },
          {
            "name": "tzdata",
            "direct": false,
            "version": "2026.3",
            "ecosystem": "pypi"
          },
          {
            "name": "urllib3",
            "direct": false,
            "version": "2.7.0",
            "ecosystem": "pypi"
          },
          {
            "name": "uvicorn",
            "direct": false,
            "version": "0.51.0",
            "ecosystem": "pypi"
          },
          {
            "name": "virtualenv",
            "direct": false,
            "version": "21.7.0",
            "ecosystem": "pypi"
          },
          {
            "name": "watchfiles",
            "direct": false,
            "version": "1.2.0",
            "ecosystem": "pypi"
          },
          {
            "name": "wcwidth",
            "direct": false,
            "version": "0.8.2",
            "ecosystem": "pypi"
          },
          {
            "name": "webencodings",
            "direct": false,
            "version": "0.5.1",
            "ecosystem": "pypi"
          },
          {
            "name": "websockets",
            "direct": false,
            "version": "16.1.1",
            "ecosystem": "pypi"
          },
          {
            "name": "werkzeug",
            "direct": false,
            "version": "3.1.8",
            "ecosystem": "pypi"
          },
          {
            "name": "widgetsnbextension",
            "direct": false,
            "version": "4.0.15",
            "ecosystem": "pypi"
          },
          {
            "name": "xgboost",
            "direct": false,
            "version": "2.1.4",
            "ecosystem": "pypi"
          },
          {
            "name": "yarl",
            "direct": false,
            "version": "1.24.5",
            "ecosystem": "pypi"
          }
        ],
        "collected": true,
        "truncated": false,
        "total_count": 210,
        "direct_count": 19,
        "indirect_count": 191
      }
    },
    "maintainership": {
      "issues": {
        "open_prs": 0,
        "merged_prs": 110,
        "open_issues": 14,
        "closed_ratio": 0.886,
        "closed_issues": 109,
        "closed_unmerged_prs": 21
      },
      "bus_factor": 2,
      "bot_contributors": 0,
      "top_contributors": [
        {
          "type": "User",
          "login": "RalfG",
          "commits": 545,
          "avatar_url": "https://avatars.githubusercontent.com/u/26458971?v=4"
        },
        {
          "type": "User",
          "login": "ArthurDeclercq",
          "commits": 368,
          "avatar_url": "https://avatars.githubusercontent.com/u/61241434?v=4"
        },
        {
          "type": "User",
          "login": "anasilviacs",
          "commits": 145,
          "avatar_url": "https://avatars.githubusercontent.com/u/17022777?v=4"
        },
        {
          "type": "User",
          "login": "rodvrees",
          "commits": 27,
          "avatar_url": "https://avatars.githubusercontent.com/u/93122887?v=4"
        },
        {
          "type": "User",
          "login": "paretje",
          "commits": 14,
          "avatar_url": "https://avatars.githubusercontent.com/u/4622838?v=4"
        },
        {
          "type": "User",
          "login": "tivdnbos",
          "commits": 11,
          "avatar_url": "https://avatars.githubusercontent.com/u/13612447?v=4"
        },
        {
          "type": "User",
          "login": "SamvPy",
          "commits": 5,
          "avatar_url": "https://avatars.githubusercontent.com/u/92147229?v=4"
        }
      ],
      "contributors_sampled": 7,
      "top_contributor_share": 0.489
    },
    "quality_signals": {
      "has_ci": true,
      "has_tests": true,
      "ci_workflows": [
        "publish.yml",
        "test.yml"
      ],
      "has_docs_dir": true,
      "linter_configs": [],
      "has_editorconfig": false,
      "has_linter_config": true,
      "has_precommit_config": true
    },
    "security_signals": {
      "lockfiles": [
        "uv.lock"
      ],
      "scorecard": {
        "checks": [
          {
            "name": "Binary-Artifacts",
            "score": 10,
            "reason": "no binaries found in the repo",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
          },
          {
            "name": "Branch-Protection",
            "score": null,
            "reason": "internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
          },
          {
            "name": "CI-Tests",
            "score": 8,
            "reason": "4 out of 5 merged PRs checked by a CI test -- score normalized to 8",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
          },
          {
            "name": "CII-Best-Practices",
            "score": 0,
            "reason": "no effort to earn an OpenSSF best practices badge detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
          },
          {
            "name": "Code-Review",
            "score": 1,
            "reason": "Found 1/7 approved changesets -- score normalized to 1",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 10,
            "reason": "project has 6 contributing companies or organizations",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": 10,
            "reason": "no dangerous workflow patterns detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
          {
            "name": "Dependency-Update-Tool",
            "score": 0,
            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
          },
          {
            "name": "Fuzzing",
            "score": 0,
            "reason": "project is not fuzzed",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
          },
          {
            "name": "License",
            "score": 10,
            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
          },
          {
            "name": "Maintained",
            "score": 10,
            "reason": "30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
          },
          {
            "name": "Packaging",
            "score": 10,
            "reason": "packaging workflow detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
          },
          {
            "name": "Pinned-Dependencies",
            "score": 1,
            "reason": "dependency not pinned by hash detected -- score normalized to 1",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "SAST tool is not run on all commits -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
          },
          {
            "name": "Security-Policy",
            "score": 0,
            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
          },
          {
            "name": "Signed-Releases",
            "score": 0,
            "reason": "Project has not signed or included provenance with any releases.",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
          },
          {
            "name": "Token-Permissions",
            "score": 0,
            "reason": "detected GitHub workflow tokens with excessive permissions",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
          {
            "name": "Vulnerabilities",
            "score": 10,
            "reason": "0 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
          }
        ],
        "commit": "7d2abba92aa99742be475a11fb9de8a81c621bdb",
        "ran_at": "2026-07-27T22:27:03Z",
        "aggregate_score": 4.7,
        "scorecard_version": "v5.5.0"
      },
      "has_codeql_workflow": false,
      "has_security_policy": false,
      "has_dependabot_config": false
    },
    "contribution_flow": {
      "collected": true,
      "ci_last_run_at": "2026-07-24T21:47:47Z",
      "oldest_open_prs": [],
      "last_merged_pr_at": "2026-07-24T21:20:39Z",
      "ci_last_conclusion": "SUCCESS",
      "oldest_open_issues": [
        {
          "number": 135,
          "created_at": "2024-03-22T15:08:36Z",
          "last_comment_at": "2025-03-18T17:31:41Z",
          "last_comment_author": "tentrillion"
        },
        {
          "number": 150,
          "created_at": "2024-05-23T10:18:31Z",
          "last_comment_at": "2024-08-08T13:48:54Z",
          "last_comment_author": "vrkosk"
        },
        {
          "number": 155,
          "created_at": "2024-07-09T11:07:32Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 158,
          "created_at": "2024-07-17T11:18:13Z",
          "last_comment_at": "2024-08-02T09:04:20Z",
          "last_comment_author": "RalfG"
        },
        {
          "number": 201,
          "created_at": "2024-10-23T13:02:50Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 202,
          "created_at": "2024-10-23T13:03:46Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 220,
          "created_at": "2025-04-09T03:09:58Z",
          "last_comment_at": "2025-12-18T13:04:13Z",
          "last_comment_author": "RalfG"
        },
        {
          "number": 227,
          "created_at": "2025-04-30T08:11:51Z",
          "last_comment_at": "2025-12-18T13:30:35Z",
          "last_comment_author": "RalfG"
        },
        {
          "number": 230,
          "created_at": "2025-07-10T14:56:20Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 255,
          "created_at": "2026-04-16T12:22:02Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 256,
          "created_at": "2026-04-18T15:54:53Z",
          "last_comment_at": null,
          "last_comment_author": null
        },
        {
          "number": 257,
          "created_at": "2026-04-21T15:23:04Z",
          "last_comment_at": "2026-07-22T11:04:54Z",
          "last_comment_author": "RalfG"
        },
        {
          "number": 271,
          "created_at": "2026-07-17T15:46:34Z",
          "last_comment_at": "2026-07-22T10:24:37Z",
          "last_comment_author": "RalfG"
        },
        {
          "number": 272,
          "created_at": "2026-07-17T16:13:44Z",
          "last_comment_at": "2026-07-22T10:21:52Z",
          "last_comment_author": "RalfG"
        }
      ]
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/CompOmics/ms2rescore",
    "host": "github.com",
    "name": "ms2rescore",
    "owner": "CompOmics"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "good",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 72,
      "inputs": {
        "security": 58,
        "vitality": 79,
        "community": 56,
        "governance": 73,
        "engineering": 90
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "good",
        "name": "Vitality",
        "value": 79,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "good",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 77,
            "inputs": {
              "commits_last_year": 210,
              "human_commit_share": 1,
              "days_since_last_push": 3,
              "active_weeks_last_year": 19
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 3 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "push_recency",
                    "params": {
                      "days": 3
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "19/52 weeks with commits",
                "points": 13.2,
                "status": "partial",
                "details": [
                  {
                    "code": "commit_cadence_weeks",
                    "params": {
                      "weeks": 19
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "210 commits in the last year",
                "points": 18,
                "status": "met",
                "details": [
                  {
                    "code": "commits_last_year",
                    "params": {
                      "count": 210
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "release_discipline",
            "band": "good",
            "name": "Release discipline",
            "note": null,
            "notes": [],
            "value": 83,
            "inputs": {
              "releases_count": 43,
              "latest_release_tag": "v4.0.1",
              "releases_from_tags": false,
              "days_since_latest_release": 3,
              "mean_days_between_releases": 78.8
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "43 releases published",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "releases_published",
                    "params": {
                      "count": 43
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "latest release 3 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "release_recency",
                    "params": {
                      "days": 3
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "a release every ~78.8 days",
                "points": 19.8,
                "status": "partial",
                "details": [
                  {
                    "code": "release_cadence",
                    "params": {
                      "gap": 78.8
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "openssf_scorecard_signed_releases",
                "name": "OpenSSF Scorecard: Signed-Releases",
                "detail": "Project has not signed or included provenance with any releases.",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "abandonment",
            "band": "excellent",
            "name": "Abandonment",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "cap": null,
              "state": "maintained",
              "guards": [],
              "signals": [],
              "red_flag": false,
              "multiplier_pct": 100,
              "declared_reason": null,
              "unverified_reason": null,
              "unanswered_open_prs": null,
              "unanswered_open_issues": null,
              "days_since_last_merged_pr": null,
              "days_since_last_human_commit": 3,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 3 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 3
                    }
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "moderate",
        "name": "Community & Adoption",
        "value": 56,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "at_risk",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 44,
            "inputs": {
              "forks": 22,
              "stars": 66,
              "watchers": 6,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "66 stars",
                "points": 29.4,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 66
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "22 forks",
                "points": 11,
                "status": "partial",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 22
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "6 watchers",
                "points": 3.9,
                "status": "partial",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 6
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "good",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 70,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": true,
              "has_issue_template": false,
              "has_code_of_conduct": false,
              "has_pull_request_template": false
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 22.5,
                "status": "met",
                "details": [],
                "max_points": 22.5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "recognized license (Apache-2.0)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "Apache-2.0"
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 18,
                "status": "met",
                "details": [],
                "max_points": 18
              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 13.5
              },
              {
                "key": "issue_template",
                "name": "Issue template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
              },
              {
                "key": "pr_template",
                "name": "PR template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.3
              }
            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
      },
      {
        "key": "governance",
        "band": "good",
        "name": "Sustainability & Governance",
        "value": 73,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "moderate",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 56,
            "inputs": {
              "bus_factor": 2,
              "contributors_sampled": 7,
              "top_contributor_share": 0.489
            },
            "components": [
              {
                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "2 contributor(s) cover half of all commits",
                "points": 25.2,
                "status": "partial",
                "details": [
                  {
                    "code": "bus_factor",
                    "params": {
                      "count": 2
                    }
                  }
                ],
                "max_points": 54
              },
              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 49% of commits",
                "points": 11.5,
                "status": "partial",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 49
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "7 contributors",
                "points": 9.5,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 7
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 6 contributing companies or organizations",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "good",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 75,
            "inputs": {
              "merged_prs": 110,
              "open_issues": 14,
              "closed_issues": 109,
              "issue_closed_ratio": 0.886,
              "closed_unmerged_prs": 21
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "89% of issues closed",
                "points": 41.4,
                "status": "partial",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 89
                    }
                  }
                ],
                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "110/131 decided PRs merged",
                "points": 32.1,
                "status": "partial",
                "details": [
                  {
                    "code": "decided_prs_merged",
                    "params": {
                      "merged": 110,
                      "decided": 131
                    }
                  }
                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 1/7 approved changesets -- score normalized to 1",
                "points": 1.5,
                "status": "partial",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "good",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 70,
            "inputs": {
              "followers": 129,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "CompOmics",
              "public_repos": 114,
              "account_age_days": 4143
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "organization-owned",
                "points": 30,
                "status": "met",
                "details": [
                  {
                    "code": "owner_organization",
                    "params": {}
                  }
                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "129 followers of CompOmics",
                "points": 15.2,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 129,
                      "login": "CompOmics"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "114 public repos, account ~11 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 114
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 11
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
                "ms2rescore"
              ],
              "ecosystems": "pypi",
              "any_deprecated": false,
              "min_days_since_publish": 3
            },
            "components": [
              {
                "key": "published_resolvable",
                "name": "Published & resolvable",
                "detail": "1 package(s) on pypi",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "packages_published",
                    "params": {
                      "count": 1,
                      "ecosystems": "pypi"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 3 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
                    "params": {
                      "days": 3
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "version_history",
                "name": "Version history",
                "detail": "45 published versions",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "published_versions",
                    "params": {
                      "count": 45
                    }
                  }
                ],
                "max_points": 20
              },
              {
                "key": "not_deprecated",
                "name": "Not deprecated",
                "detail": "active, not deprecated or yanked",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "package_not_deprecated",
                    "params": {}
                  }
                ],
                "max_points": 20
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "excellent",
        "name": "Engineering Quality",
        "value": 90,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "excellent",
            "name": "Engineering practices",
            "note": null,
            "notes": [],
            "value": 90,
            "inputs": {
              "has_ci": true,
              "has_tests": true,
              "has_editorconfig": false,
              "has_linter_config": true,
              "has_precommit_config": true
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "2 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 2
                    }
                  }
                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 24,
                "status": "met",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 16,
                "status": "met",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 9.6,
                "status": "met",
                "details": [],
                "max_points": 9.6
              },
              {
                "key": "editorconfig",
                "name": ".editorconfig",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "4 out of 5 merged PRs checked by a CI test -- score normalized to 8",
                "points": 16,
                "status": "partial",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 90,
            "inputs": {
              "topics": [
                "proteomics",
                "ms2pip",
                "percolator",
                "deeplc",
                "peptide-identification"
              ],
              "has_wiki": false,
              "homepage": "https://ms2rescore.readthedocs.io",
              "has_readme": true,
              "has_docs_dir": true,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 25,
                "status": "met",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": "https://ms2rescore.readthedocs.io",
                "points": 15,
                "status": "met",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "5 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "moderate",
        "name": "Security",
        "value": 58,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Branch-Protection. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "branch_protection"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 47,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 17,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 1,
              "scorecard_aggregate": 4.7
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "branch_protection",
                "name": "Branch-Protection",
                "detail": "internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "4 out of 5 merged PRs checked by a CI test -- score normalized to 8",
                "points": 2,
                "status": "partial",
                "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 1/7 approved changesets -- score normalized to 1",
                "points": 0.8,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 6 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 5 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 1",
                "points": 0.5,
                "status": "partial",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "Project has not signed or included provenance with any releases.",
                "points": 0,
                "status": "missed",
                "details": [],
                "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": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "excellent",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:ms2rescore@4.0.1 runtime dependency closure — what installing the published package pulls in — 69 packages. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "no_advisories_left_outstanding"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_published",
                "params": {
                  "package": "pypi:ms2rescore@4.0.1",
                  "assessed": 69
                }
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "source": "osv",
              "advisories": 0,
              "affected_packages": 0,
              "assessed_packages": 69,
              "unassessed_packages": 0,
              "affected_by_severity": "none",
              "direct_affected_packages": 0
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "no direct dependency carries a known advisory",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "no_direct_advisories",
                    "params": {}
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "no indirect dependency carries a known advisory",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "no_indirect_advisories",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory carries a publication date",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_no_publication_date",
                    "params": {}
                  }
                ],
                "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": 69,
              "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": 6
            },
            "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": "at_risk",
        "name": "AI Readiness",
        "value": 43,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "at_risk",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 32,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.6,
              "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": "60 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 32,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 60,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "at_risk",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 48,
            "inputs": {
              "has_nix": false,
              "has_tests": true,
              "lockfiles": [
                "uv.lock"
              ],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": true,
              "typecheck_configs": [],
              "agent_commit_share": 0.02,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "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": "2 of the last 100 commits agent-authored or agent-credited",
                "points": 4,
                "status": "partial",
                "details": [
                  {
                    "code": "agent_authored_commits",
                    "params": {
                      "count": 2,
                      "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 1",
                "points": 1,
                "status": "partial",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 54,
            "inputs": {
              "primary_language": "Python",
              "largest_source_bytes": 116571,
              "source_files_sampled": 49,
              "oversized_source_files": 1
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Python without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "Python"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "1/49 source files over 60KB",
                "points": 53.9,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 49,
                      "oversized": 1
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          },
          {
            "key": "ai_interfaces",
            "band": "at_risk",
            "name": "Machine-readable interfaces",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "example_dirs": [
                "examples",
                "notebooks"
              ],
              "has_mcp_signal": false,
              "api_schema_files": []
            },
            "components": [
              {
                "key": "api_schema_openapi_graphql_proto",
                "name": "API schema (OpenAPI/GraphQL/proto)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 40
              },
              {
                "key": "mcp_server",
                "name": "MCP server",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "runnable_examples",
                "name": "Runnable examples",
                "detail": "examples, notebooks",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "examples, notebooks"
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          }
        ],
        "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": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-27T22:27:21.075230Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/CompOmics/ms2rescore.svg",
  "full_name": "CompOmics/ms2rescore",
  "license_state": "standard",
  "license_spdx": "Apache-2.0"
}