CompOmics / ms2rescore

Wann jeder Stern und Fork hinzugefügt wurde, von GitHub erfasst und nach Tagen gruppiert. Das kumulierte Wachstum steht direkt über den täglichen Zugängen, aus denen es besteht, sodass beide gegeneinander lesbar sind: stetiger organischer Zuwachs sieht ganz anders aus als ein abrupter, kurzlebiger Ausschlag. Wo dieser Unterschied messbar ist, wird er als Wachstumsauthentizität ausgewiesen.

Jeder Punkt umfasst 7 Tage.

Vollständig aufgelöster Abhängigkeitssatz aus dem GitHub-Abhängigkeitsgraphen: 19 direkte und 191 indirekte (transitive) Pakete. Die transitive Hülle ist vollständig, wenn das Repository eine Lockfile eincheckt.

Die Installation von pypi:ms2rescore@4.0.1 zieht 69 Pakete nach sich, direkt und transitiv: 0 tragen bekannte Advisories, davon 0 direkte Abhängigkeiten.

Keine bekannten Advisories betreffen die bewerteten Abhängigkeiten.

Ein Advisory bedeutet, dass die im Abhängigkeitsgraphen erfasste Version in den betroffenen Bereich eines Advisories fällt. Erreichbarkeit wird nicht analysiert, und der Graph enthält Entwicklungs- und Test-Pins — ein Fund kann das Werkzeug betreffen und nicht die ausgelieferte Software.

{
  "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"
}