Öffentliches Register
Software-GesundheitsberichtSchema 0.27.0 · Metriken 2.3.1 · 2026-08-01 12:19 UTC

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

RGPL-3.0★ 214 Sterne⑂ 103 Forksseit Jan. 2017Auf GitHub ansehen ↗

broadinstitute/ichorCNA erreicht einen Gesundheitsindex von 16 von 100 und liegt damit im Bereich Kritisch. Am stärksten schneidet es bei Community & Adoption (63/100) ab, am schwächsten bei AI Readiness (5/100). Zuletzt vor 863 Tagen aktualisiert. Ein einzelner Mitwirkender trägt den Großteil der jüngsten Arbeit.

16
gesamt / 100
Kritisch

Software-Gesundheitsindex

Metriken werden auf einer standardisierten Skala von 1–100 in gewichtete Kategorien gruppiert. Der Gesamtwert beginnt als ihr gewichtetes Mittel, kalibriert auf die Verteilung des öffentlichen Registers, sodass die Stufen Perzentilbedeutung tragen; sobald öffentliche Evidenz die Richtlinie für Hochrisikojurisdiktionen auslöst, wird die Bewertung angepasst und erhält die Obergrenze Gefährdet von 34.

16
Außergewöhnlich93-100Die Spitzengruppe des Registers (≈ obere 5 %); erfüllt im Wesentlichen alle geprüften Kriterien
Exzellent80-92Durchgehend stark; geringfügige Lücken
Gut65-79Gesund; Lücken sind begrenzt und beherrschbar
Mittel50-64Akzeptabel mit deutlichen Lücken; Überprüfung empfohlen
Schwach35-49Wesentliche Schwächen in mehreren Bereichen
Gefährdet20-34Erhebliche Schwächen; eine Übernahme erfordert Vorsicht
Kritisch1-19Schwerwiegende Probleme (aufgegeben, nur ein Maintainer, keine Hygiene)
VitalitätCommunity &VerbreitungNachhaltigkeit &GovernanceEngineering-QualitätSicherheitAI Readiness

Bewertungsprofil

Jede Achse ist eine Kategorie. Die Form zählt mehr als der Durchschnitt — ein gesundes Projekt füllt die gesamte Fläche, während ein Profil aus Spitzen und Kratern bedeutet, dass Stärke in einer Dimension Risiken in einer anderen verdeckt.

Der gewichtete Gesamtwert 33 wird auf der veröffentlichten Indexskala auf 27 kalibriert (Register-Kalibrierung 2026-08-02).

Eigentümerschaft

Broad InstituteOrganisation
1.290 Follower1.515 öffentliche Reposseit Sept. 2010

Dieses Repository wird von einer Organisation getragen — geteilte, rechenschaftspflichtige Trägerschaft, die jeden einzelnen Maintainer überdauern kann.

Metriken nach Kategorie

Vitalität

Lebt das Projekt — wird Code geschrieben und werden Releases ausgeliefert?

15Kritisch · 21 % des Gesamtindex
Wie die Bewertung erfolgt
0/36Push-Aktualität — letzter Push vor 863 Tagen
0/36Commit-Rhythmus — 0/52 Wochen mit Commits
0/18Commit-Volumen — 0 Commits im letzten Jahr
0/10OpenSSF Scorecard: Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
Verwendete Eingangsdaten
commits_last_year0
human_commit_share1
days_since_last_push863
active_weeks_last_year0
Wie die Bewertung erfolgt
27/27Liefert Releases aus — 2 Releases veröffentlicht
0/36Release-Aktualität — letztes Release vor 2.637 Tagen
5.4/27Release-Rhythmus — ein Release etwa alle 640,3 Tage
0/10OpenSSF Scorecard: Signed-Releases — keine Daten
Verwendete Eingangsdaten
releases_count2
latest_release_tagv0.2.0
releases_from_tagsnein
days_since_latest_release2.637
mean_days_between_releases640,3
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: Signed-Releases. Die verbleibenden Gewichte wurden renormalisiert.

Community & Verbreitung

Hat das Projekt Nutzer, Downloads, Aufmerksamkeit und ein einladendes Umfeld für Beitragende?

63Mittel · 17 % des Gesamtindex
Wie die Bewertung erfolgt
37.8/60Stars — 214 Stars
16.7/25Forks — 103 Forks
6.8/15Watcher — 18 Watcher
Verwendete Eingangsdaten
forks103
stars214
watchers18
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
Wie die Bewertung erfolgt
22.5/22.5README
22.5/22.5Lizenz — anerkannte Lizenz (GPL-3.0)
0/18CONTRIBUTING-Leitfaden
13.5/13.5Verhaltenskodex
0/7.2Issue-Vorlage
0/6.3PR-Vorlage
Verwendete Eingangsdaten
has_readmeja
has_licenseja
readme_badges
has_contributingnein
has_issue_templatenein
has_code_of_conductja
readme_badge_services
has_pull_request_templatenein

Nachhaltigkeit & Governance

Überdauert das Projekt die Menschen, die es tragen — Bus-Faktor, Reaktionsfähigkeit, Trägerschaft und Paketpflege?

39Schwach · 23 % des Gesamtindex
Wie die Bewertung erfolgt
9/54Bus-Faktor — 1 Beitragende decken die Hälfte aller Commits ab
6.5/22.5Commit-Verteilung — wichtigste beitragende Person verfasste 71 % der Commits
2.7/13.5Breite der Beitragenden — 2 Beitragende
10/10OpenSSF Scorecard: Contributors — project has 3 contributing companies or organizations -- score normalized to 10
Verwendete Eingangsdaten
bus_factor1
contributors_sampled2
top_contributor_share0,709
Wie die Bewertung erfolgt
12.7/42Issue-Lösungsquote — 30 % der Issues geschlossen
0/30PR-Annahme — 0/6 entschiedene PRs gemergt
0/13Newcomer PR acceptance — kein PR eines Erstbeitragenden in 30 Tagen entschieden
0/15OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0
Verwendete Eingangsdaten
merged_prs0
open_issues97
closed_issues42
prs_merged_7d
prs_decided_7d
prs_merged_30d
prs_decided_30d
issue_closed_ratio0,302
closed_unmerged_prs6
first_time_authors_30d
first_time_prs_merged_30d
first_time_prs_decided_30d
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): newcomer_pr_acceptance. Die verbleibenden Gewichte wurden renormalisiert.
Wie die Bewertung erfolgt
30/30Organisatorische Trägerschaft — im Besitz einer Organisation
0/20Verifizierte Domain
22.4/25Reichweite des Inhabers — 1.290 Follower von broadinstitute
25/25Kontohistorie — 1.515 öffentliche Repos, Kontoalter ca. 15 Jahre
Verwendete Eingangsdaten
followers1.290
owner_typeOrganization
is_verified
owner_loginbroadinstitute
public_repos1.515
account_age_days5.804

Engineering-Qualität

Sind grundlegende Engineering- und Dokumentationspraktiken vorhanden?

25Gefährdet · 19 % des Gesamtindex
Wie die Bewertung erfolgt
0/24CI-Workflows
0/24Tests vorhanden
0/16Linter-Konfiguration
0/9.6Pre-Commit-Hooks
0/6.4.editorconfig
0/20OpenSSF Scorecard: CI-Tests — keine Daten
Verwendete Eingangsdaten
has_cinein
has_testsnein
has_editorconfignein
has_linter_confignein
has_precommit_confignein
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: CI-Tests. Die verbleibenden Gewichte wurden renormalisiert.
Wie die Bewertung erfolgt
30/30README
0/25Dokumentationsverzeichnis
0/15Dokumentations-/Homepage-Site
10/10Repository-Beschreibung
10/10Topics — 3 Topics
10/10Wiki
Verwendete Eingangsdaten
topicscopy-number, low-coverage-sequencing, cell-free-dna
has_wikija
homepage
has_readmeja
has_docs_dirnein
has_descriptionja

Sicherheit

Sind die sichtbaren Sicherheits- und Lieferkettenpraktiken belastbar, ohne ungeklärte Exposition gegenüber Hochrisikojurisdiktionen?

30Gefährdet · 16 % des Gesamtindex

Sicherheitslage

30Gefährdet
Wie die Bewertung erfolgt
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
0/2.5CI-Tests — keine Daten
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/30 approved changesets -- score normalized to 0
2.5/2.5Contributors — project has 3 contributing companies or organizations -- score normalized to 10
0/10Dangerous-Workflow — keine Daten
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5Lizenz — license file detected
0/7.5Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
0/5Packaging — keine Daten
0/5Pinned-Dependencies — keine Daten
0/5SAST — no SAST tool detected
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — keine Daten
0/7.5Token-Permissions — keine Daten
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Verwendete Eingangsdaten
sourceopenssf_scorecard
checks_evaluated12
scorecard_versionv5.5.0
checks_inconclusive6
scorecard_aggregate3
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): ci_tests, dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Die verbleibenden Gewichte wurden renormalisiert.

AI Readiness

Wie gut ist das Repository dafür ausgestattet, mit KI-Coding-Agenten entwickelt und gepflegt zu werden? Trägt ein bewusst kleines Gewicht (4 %): Agenten-Tooling ist ein echtes Pflegesignal, doch ein Repository ohne jedes Signal kann weiterhin 100/100 erreichen.

5Kritisch · 4 % des Gesamtindex
Wie die Bewertung erfolgt
0/45Agentenanweisungen — keine CLAUDE.md / AGENTS.md / Editor-Regeln
0/15Maschinenlesbare Doku (llms.txt)
12.3/40Lesbare Commit-Historie — 23 von 100 menschlichen Commits benennen ihre Absicht (strukturierter Betreff oder erläuternder Text)
Verwendete Eingangsdaten
has_llms_txtnein
legible_history_share0,23
agent_instruction_files
agent_instruction_max_bytes
Wie die Bewertung erfolgt
0/18Bootstrap mit einem Befehl
0/22Automatisierte Tests
0/11Lint-/Format-Konfiguration
0/11Statische Typprüfung
0/10Reproduzierbare Umgebung
0/10Belegte Agentenpraxis — keine von Agenten verfassten Commits unter den letzten 100
0/8Automatisierte Wartung — keine automatisierten Abhängigkeits-Updates beobachtet
0/10OpenSSF Scorecard: Pinned-Dependencies — keine Daten
Verwendete Eingangsdaten
has_nixnein
has_testsnein
lockfiles
has_dockerfilenein
typed_languagenein
bootstrap_files
has_devcontainernein
has_linter_confignein
typecheck_configs
agent_commit_share0
toolchain_manifests
dependency_bot_commit_share0
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: Pinned-Dependencies. Die verbleibenden Gewichte wurden renormalisiert.
Wie die Bewertung erfolgt
0/45Typprüfbarer Code — R ohne Typprüfungs-Konfiguration
0/55Handhabbare Dateigrößen — keine Quelldateien erkannt
Verwendete Eingangsdaten
primary_languageR
largest_source_bytes
source_files_sampled0
oversized_source_files0
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): Handhabbare Dateigrößen. Die verbleibenden Gewichte wurden renormalisiert.

Eckdaten

214GitHub-Sterne
2Mitwirkende
0Commits, letzte 12 Monate
863Tage seit letztem Push
2Releases
1Bus-Faktor
97offene Issues
Paket-Ökosysteme

Warnungen zur Datenerhebung

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository

Weitere Details

Stern- und Fork-Verlauf 0 ★ / 103 ⇿
0Sterne
103Forks
1Releases

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.

0204060801008822017-112022-032026-07
Major 0Minor 1Patch 0

Jeder Punkt umfasst 8 Tage.

OpenSSF Scorecard 3.0 / 10
3.0Gesamtwert

Unabhängige, werkzeugneutrale Sicherheitsbewertung durch das quelloffene OpenSSF Scorecard. Jede Prüfung honoriert eine Sicherheits-Praxis, nicht das Werkzeug eines bestimmten Anbieters. Prüfungen, die Scorecard nicht ermitteln konnte, sind mit k. A. markiert und vom Sicherheitswert ausgeschlossen (nie als null gezählt).Scorecard v5.5.0 · 2026-08-01 12:19 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
k. A.CI-Testsno pull request found
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/30 approved changesets -- score normalized to 0
10Contributorsproject has 3 contributing companies or organizations -- score normalized to 10
k. A.Dangerous-Workflowno workflows found
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
0Maintained0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
k. A.Packagingpackaging workflow not detected
k. A.Pinned-Dependenciesno dependencies found
0SASTno SAST tool detected
0Security-Policysecurity policy file not detected
k. A.Signed-Releasesno releases found
k. A.Token-PermissionsNo tokens found
10Vulnerabilities0 existing vulnerabilities detected
Alle Abhängigkeiten nicht erhoben

Der aufgelöste Abhängigkeitssatz konnte für diesen Bericht nicht erhoben werden: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository

JSON-Rohbericht maschinenlesbar
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          "type": "User",
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          "avatar_url": "https://avatars.githubusercontent.com/u/15793246?v=4"
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      "top_contributor_share": 0.709
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      "ci_workflows": [],
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          },
          {
            "name": "Token-Permissions",
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            "reason": "No tokens found",
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          },
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            "name": "Vulnerabilities",
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            "reason": "0 existing vulnerabilities detected",
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          "number": 15,
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          "last_comment_at": "2018-05-18T12:55:15Z",
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          "number": 25,
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              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 71% of commits",
                "points": 6.5,
                "status": "partial",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 71
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "2 contributors",
                "points": 2.7,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 2
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 3 contributing companies or organizations -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "critical",
            "name": "Issue & PR responsiveness",
            "note": "Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "newcomer_pr_acceptance"
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 15,
            "inputs": {
              "merged_prs": 0,
              "open_issues": 97,
              "closed_issues": 42,
              "prs_merged_7d": null,
              "prs_decided_7d": null,
              "prs_merged_30d": null,
              "prs_decided_30d": null,
              "issue_closed_ratio": 0.302,
              "closed_unmerged_prs": 6,
              "first_time_authors_30d": null,
              "first_time_prs_merged_30d": null,
              "first_time_prs_decided_30d": null
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "30% of issues closed",
                "points": 12.7,
                "status": "partial",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 30
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                  }
                ],
                "max_points": 42
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "0/6 decided PRs merged",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "decided_prs_merged",
                    "params": {
                      "merged": 0,
                      "decided": 6
                    }
                  }
                ],
                "max_points": 30
              },
              {
                "key": "newcomer_pr_acceptance",
                "name": "Newcomer PR acceptance",
                "detail": "no first-time contributor's PR decided in 30d",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_newcomer_prs",
                    "params": {
                      "days": 30
                    }
                  }
                ],
                "max_points": 13
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 0/30 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "good",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 77,
            "inputs": {
              "followers": 1290,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "broadinstitute",
              "public_repos": 1515,
              "account_age_days": 5804
            },
            "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": "1,290 followers of broadinstitute",
                "points": 22.4,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 1290,
                      "login": "broadinstitute"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "1515 public repos, account ~15 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 1515
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 15
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "at_risk",
        "name": "Engineering Quality",
        "value": 25,
        "weight": 0.19,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "critical",
            "name": "Engineering practices",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: CI-Tests. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_ci_tests"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
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            ],
            "value": 1,
            "inputs": {
              "has_ci": false,
              "has_tests": false,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 0,
                "status": "missed",
                "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": "no pull request found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "moderate",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 60,
            "inputs": {
              "topics": [
                "copy-number",
                "low-coverage-sequencing",
                "cell-free-dna"
              ],
              "has_wiki": true,
              "homepage": null,
              "has_readme": true,
              "has_docs_dir": false,
              "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": 0,
                "status": "missed",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": null,
                "points": 0,
                "status": "missed",
                "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": "3 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "at_risk",
        "name": "Security",
        "value": 30,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): CI-Tests, Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "ci_tests",
                    "dangerous_workflow",
                    "packaging",
                    "pinned_dependencies",
                    "signed_releases",
                    "token_permissions"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 30,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 12,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 6,
              "scorecard_aggregate": 3
            },
            "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": "branch protection not enabled on development/release branches",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "no pull request found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "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 0/30 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 3 contributing companies or organizations -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no workflows found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "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": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "no SAST tool detected",
                "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": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "No tokens found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "exceptional",
            "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"
              ],
              "commit_weight_rule": {
                "min_commits": 50,
                "min_commit_share": 0.1
              },
              "review_only_matches": 0,
              "below_threshold_exposures": [],
              "assessed_self_published_locations": 2
            },
            "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": "critical",
        "name": "AI Readiness",
        "value": 5,
        "weight": 0.04,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 12,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.23,
              "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": "23 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 12.3,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 23,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "critical",
            "name": "Verify loop (build / test / typecheck)",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_pinned_dependencies"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 1,
            "inputs": {
              "has_nix": false,
              "has_tests": false,
              "lockfiles": [],
              "has_dockerfile": false,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [],
              "agent_commit_share": 0,
              "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": 0,
                "status": "missed",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "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": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no agent-authored commits among the last 100",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_authored_commits",
                    "params": {
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "critical",
            "name": "Code legibility for models",
            "note": "Excluded from scoring (no data or not applicable): Manageable file sizes. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "manageable_file_sizes"
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
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            ],
            "value": 1,
            "inputs": {
              "primary_language": "R",
              "largest_source_bytes": null,
              "source_files_sampled": 0,
              "oversized_source_files": 0
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "R without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "R"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "no source files detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_source_files",
                    "params": {}
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight: agent tooling is a real maintenance signal, but its absence must never gate the top of the scale (calibration saturates at raw 91, so 100/100 remains reachable with AI Readiness at zero)."
      }
    ],
    "classification": {
      "labels": [],
      "scores": {},
      "primary": null,
      "evidence": [],
      "artifacts": [],
      "confidence": "none",
      "host_extension": false,
      "runs_as_process": false,
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    "metrics_version": "2.3.1"
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  "warnings": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token",
    "GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository"
  ],
  "report_type": "repository",
  "generated_at": "2026-08-01T12:19:46.628283Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/b/broadinstitute/ichorCNA.svg",
  "full_name": "broadinstitute/ichorCNA",
  "license_state": "standard",
  "license_spdx": "GPL-3.0"
}

Bewertungen sind Signale, keine Garantien. Sie spiegeln öffentlich sichtbare Praxis auf GitHub wider — kein Code-Audit und keine Sicherheitsgarantie.

Fehlende Daten werden ausgeschlossen und die Gewichte neu normiert, nie als null bewertet. Die Methodik ist versioniert und offen: Metriken v2.3.1, Schema v0.27.0 — vollständige Methodik · Metriken-Wiki.

Wie ein einzelnes Ergebnis im Gesamtregister steht: aggregierte Statistiken.