Registro público
Informe de salud del softwareesquema 0.27.0 · métricas 1.13.0 · 2026-07-30 20:15 UTC

niekwit / damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

Python · RMIT★ 5 estrellas⑂ 1 forkdesde oct 2023Ver en GitHub ↗

niekwit/damid-seq tiene un índice de salud de 51 sobre 100, lo que lo sitúa en la banda Moderado. Su puntuación más alta es Vitality (62/100) y la más baja, AI Readiness (17/100). Se actualizó por última vez hace 31 días. Una sola persona concentra la mayor parte del trabajo reciente.

51
global / 100
Moderado

Índice de salud del software

Las métricas se agrupan en categorías ponderadas sobre una escala de 1 a 100. El resultado global parte de su media; cuando la evidencia pública activa la Política de Jurisdicciones de Alto Riesgo, la calificación se ajusta y recibe el límite 49 (En riesgo). Preparación para IA queda fuera.

51
Excelente85-100Ejemplar; cumple prácticamente todos los criterios evaluados
Bueno70-84Saludable; carencias menores
Moderado50-69Aceptable con carencias notables; se recomienda revisión
En riesgo30-49Debilidades significativas; su adopción exige cautela
Crítico1-29Problemas graves (proyecto abandonado, un solo mantenedor, sin higiene)
VitalidadComunidad yAdopciónSostenibilidady GobernanzaCalidad deIngenieríaSeguridadPreparaciónpara IA

Perfil de puntuación

Cada eje es una categoría. La forma importa más que la media: un proyecto sano llena toda la figura, mientras que un perfil de picos y cráteres indica que la fortaleza en una dimensión enmascara el riesgo en otra.

Titularidad

Niek WitCuenta personal
11 seguidores60 repositorios públicosdesde jul 2018University of Cambridge

Este repositorio pertenece a una cuenta personal. Un proyecto con un único propietario conlleva más riesgo de continuidad que uno respaldado por una organización.

Métricas por categoría

Vitalidad

¿Está vivo el proyecto: se escribe código y se publican versiones?

62Moderado · 22% del índice global
Cómo se puntúa
18/36Recencia de push — último push hace 31 días
3.5/36Cadencia de commits — 5/52 semanas con commits
16.2/18Volumen de commits — 62 commits en el último año
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Datos de entrada utilizados
commits_last_year62
human_commit_share1
days_since_last_push31
active_weeks_last_year5
Cómo se puntúa
27/27Publica versiones — 5 versiones publicadas
36/36Recencia de las versiones — última versión hace 31 días
12.6/27Cadencia de publicación — una versión cada ~212,4 días
0/10OpenSSF Scorecard: Signed-Releases — sin datos
Datos de entrada utilizados
releases_count5
latest_release_tagv0.7.0
releases_from_tagsno
days_since_latest_release31
mean_days_between_releases212,4
Excluidos de la puntuación (sin datos o no aplicable): OpenSSF Scorecard: Signed-Releases. Los pesos restantes se han renormalizado.

Comunidad y Adopción

¿Tiene el proyecto usuarios, descargas, atención y unas condiciones acogedoras para quienes contribuyen?

29Crítico · 18% del índice global
Cómo se puntúa
9.8/60Estrellas — 5 estrellas
0/25Forks — 1 forks
0/15Observadores — 1 observadores
Datos de entrada utilizados
forks1
stars5
watchers1
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
Cómo se puntúa
22.5/22.5README
22.5/22.5Licencia — licencia reconocida (MIT)
0/18Guía CONTRIBUTING
0/13.5Código de conducta
0/7.2Plantilla de issues
0/6.3Plantilla de PR
Datos de entrada utilizados
has_readme
has_license
has_contributingno
has_issue_templateno
has_code_of_conductno
has_pull_request_templateno

Sostenibilidad y Gobernanza

¿Sobrevivirá el proyecto a sus personas: factor bus, capacidad de respuesta, quién lo respalda y mantenimiento del paquete?

48En riesgo · 24% del índice global
Cómo se puntúa
9/54Factor bus — la mitad de los commits recae en 1 contribuyente(s)
0/22.5Distribución de commits — el principal contribuyente firma el 100% de los commits
1.4/13.5Amplitud de contribuyentes — 1 contribuyentes
3/10OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3
Datos de entrada utilizados
bus_factor1
contributors_sampled1
top_contributor_share1
Cómo se puntúa
46.8/46.8Resolución de issues — 100% de issues cerradas
38.2/38.3Aceptación de PR — 1/1 PR decididos fusionados
0/15OpenSSF Scorecard: Code-Review — Found 0/16 approved changesets -- score normalized to 0
Datos de entrada utilizados
merged_prs1
open_issues0
closed_issues1
issue_closed_ratio1
closed_unmerged_prs0
Cómo se puntúa
10/30Respaldo de la propiedad — cuenta personal (usuario)
0/20Dominio verificado — no aplicable a cuentas de usuario
7.8/25Alcance del propietario — 11 seguidores de niekwit
25/25Trayectoria — 60 repos públicos, cuenta de ~8 años
Datos de entrada utilizados
followers11
owner_typeUser
is_verified
owner_loginniekwit
public_repos60
account_age_days2936
Excluidos de la puntuación (sin datos o no aplicable): Dominio verificado. Los pesos restantes se han renormalizado.

Calidad de Ingeniería

¿Existen unas prácticas mínimas de ingeniería y documentación?

60Moderado · 20% del índice global
Cómo se puntúa
24/24Flujos de trabajo de CI — 3 flujo(s) de trabajo
0/24Pruebas presentes
0/16Configuración de linter
0/9.6Hooks de pre-commit
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
Datos de entrada utilizados
has_ci
has_testsno
has_editorconfigno
has_linter_configno
has_precommit_configno

Documentación

85Excelente
Cómo se puntúa
30/30README
25/25Directorio de documentación
0/15Sitio de documentación / página del proyecto
10/10Descripción del repositorio
10/10Topics — 3 topics
10/10Wiki
Datos de entrada utilizados
topicsbioinformatics-pipeline, damid, snakemake-workflow
has_wiki
homepage
has_readme
has_docs_dir
has_description

Seguridad

¿Son sólidas las prácticas visibles de seguridad y de cadena de suministro, sin exposición jurisdiccional de alto riesgo sin resolver?

53Moderado · 16% del índice global
Cómo se puntúa
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
2.5/2.5CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/16 approved changesets -- score normalized to 0
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5Licencia — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — sin datos
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — sin datos
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Datos de entrada utilizados
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4,1
Excluidos de la puntuación (sin datos o no aplicable): packaging, signed_releases. Los pesos restantes se han renormalizado.
Cómo se puntúa
35/35Dependencias directas libres de avisos conocidos — ninguna dependencia directa tiene un aviso conocido
0/25Dependencias indirectas libres de avisos conocidos — el conjunto transitivo no es separable de las dependencias de desarrollo y prueba en este alcance
0/40Sin avisos pendientes — ningún aviso tiene fecha de publicación
Datos de entrada utilizados
sourceosv
advisories0
affected_packages0
assessed_packages2
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluidos de la puntuación (sin datos o no aplicable): Dependencias indirectas libres de avisos conocidos, Sin avisos pendientes. Los pesos restantes se han renormalizado. Se cotejaron 2 dependencias resueltas con OSV. Este repositorio no publica ningún paquete que el índice resuelva, por lo que se evaluó en su lugar el grafo de dependencias del repositorio. Ese grafo mezcla fijaciones de desarrollo y prueba con las dependencias distribuidas, de modo que solo se puntúan las dependencias declaradas en tiempo de ejecución; los hallazgos transitivos se informan como contexto y quedan excluidos de la puntuación. No se analiza la alcanzabilidad.

Preparación para IA

¿Hasta qué punto está el repositorio preparado para desarrollarse y mantenerse con agentes de codificación de IA? Es una insignia independiente y experimental — peso 0,0, de modo que se presenta por separado y no afecta a la puntuación de salud global.

17Crítico · 0% del índice global
Cómo se puntúa
0/45Instrucciones para agentes — sin CLAUDE.md / AGENTS.md / reglas de editor
0/15Documentación legible por máquinas (llms.txt)
1.6/40Historial de commits legible — 3 de 100 commits humanos declaran su intención (asunto estructurado o cuerpo explicativo)
Datos de entrada utilizados
has_llms_txtno
legible_history_share0,03
agent_instruction_files
agent_instruction_max_bytes
Cómo se puntúa
0/18Arranque con un solo comando
0/22Pruebas automatizadas
0/11Configuración de lint / formato
0/11Verificación estática de tipos
10/10Entorno reproducible — Dockerfile
4/10Práctica demostrada con agentes — 2 de los últimos 100 commits con autoría o crédito de agente
0/8Mantenimiento automatizado — no se observan actualizaciones automáticas de dependencias
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Datos de entrada utilizados
has_nixno
has_testsno
lockfiles
has_dockerfile
typed_languageno
bootstrap_files
has_devcontainerno
has_linter_configno
typecheck_configs
agent_commit_share0,02
toolchain_manifests
dependency_bot_commit_share0
Cómo se puntúa
0/45Código verificable por tipos — Python sin configuración de verificación de tipos
55/55Tamaños de archivo manejables — 0/15 archivos fuente de más de 60 KB
Datos de entrada utilizados
primary_languagePython
largest_source_bytes3693
source_files_sampled15
oversized_source_files0

Datos clave

5estrellas de GitHub
1contribuidores
62commits en los últimos 12 meses
31días desde el último push
5versiones publicadas
1factor bus
0issues abiertas
PyPIecosistemas de paquetes

Advertencias de recopilación de datos

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

Más detalle

OpenSSF Scorecard 4.1 / 10
4.1agregado

Evaluación de seguridad independiente y agnóstica en cuanto a herramientas, procedente del proyecto de código abierto OpenSSF Scorecard. Cada comprobación premia una práctica de seguridad, no la herramienta de un proveedor concreto. Las comprobaciones que Scorecard no pudo determinar se marcan como n/d y se excluyen de la puntuación de seguridad (nunca se cuentan como cero).Scorecard v5.5.0 · 2026-07-30 20:15 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
10CI-Tests1 out of 1 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/16 approved changesets -- score normalized to 0
3Contributorsproject has 1 contributing companies or organizations -- score normalized to 3
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
n/dPackagingpackaging workflow not detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/dSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
Todas las dependencias 2

Conjunto completo de dependencias resueltas según el grafo de dependencias de GitHub: 0 paquetes directos y 2 indirectos (transitivos). El cierre transitivo es completo cuando el repositorio incluye un lockfile.

RegistroPaqueteVersiónRelación
PyPIsphinx7.3.7indirecta
PyPIsphinx-rtd-theme2.0.0indirecta
Avisos de dependencias 0

Este repositorio no publica ningún paquete que el índice resuelva, así que se evaluó su propio grafo de dependencias — 2 paquetes, que incluyen también fijaciones de desarrollo y prueba que nunca se distribuyen: 0 tienen avisos conocidos, de los cuales 0 son directas.

Ningún aviso conocido afecta a las dependencias evaluadas.

Un aviso significa que la versión registrada en el grafo de dependencias cae dentro del rango afectado de un aviso. No se analiza la alcanzabilidad, y el grafo incluye fijaciones de desarrollo y prueba: un hallazgo puede referirse al utillaje y no al software distribuido.

Informe JSON sin procesar legible por máquina
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                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 0 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": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 84,
            "inputs": {
              "releases_count": 5,
              "latest_release_tag": "v0.7.0",
              "releases_from_tags": false,
              "days_since_latest_release": 31,
              "mean_days_between_releases": 212.4
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "5 releases published",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "releases_published",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "latest release 31 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "release_recency",
                    "params": {
                      "days": 31
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "a release every ~212.4 days",
                "points": 12.6,
                "status": "partial",
                "details": [
                  {
                    "code": "release_cadence",
                    "params": {
                      "gap": 212.4
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "openssf_scorecard_signed_releases",
                "name": "OpenSSF Scorecard: Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "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": 35,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 35 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 35
                    }
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "critical",
        "name": "Community & Adoption",
        "value": 29,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "critical",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 10,
            "inputs": {
              "forks": 1,
              "stars": 5,
              "watchers": 1,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "5 stars",
                "points": 9.8,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "1 forks",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "1 watchers",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "moderate",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": false,
              "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 (MIT)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "MIT"
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 0,
                "status": "missed",
                "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": "at_risk",
        "name": "Sustainability & Governance",
        "value": 48,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "critical",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 13,
            "inputs": {
              "bus_factor": 1,
              "contributors_sampled": 1,
              "top_contributor_share": 1
            },
            "components": [
              {
                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "1 contributor(s) cover half of all commits",
                "points": 9,
                "status": "partial",
                "details": [
                  {
                    "code": "bus_factor",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 54
              },
              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 100% of commits",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
                "points": 1.4,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 3,
                "status": "partial",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "excellent",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "merged_prs": 1,
              "open_issues": 0,
              "closed_issues": 1,
              "issue_closed_ratio": 1,
              "closed_unmerged_prs": 0
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "100% of issues closed",
                "points": 46.8,
                "status": "met",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "1/1 decided PRs merged",
                "points": 38.2,
                "status": "met",
                "details": [
                  {
                    "code": "decided_prs_merged",
                    "params": {
                      "merged": 1,
                      "decided": 1
                    }
                  }
                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 0/16 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "moderate",
            "name": "Ownership & stewardship",
            "note": "Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "verified_domain"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 54,
            "inputs": {
              "followers": 11,
              "owner_type": "User",
              "is_verified": null,
              "owner_login": "niekwit",
              "public_repos": 60,
              "account_age_days": 2936
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "personal (user) account",
                "points": 10,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_personal",
                    "params": {}
                  }
                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": "not applicable to user accounts",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "not_applicable_to_user_accounts",
                    "params": {}
                  }
                ],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "11 followers of niekwit",
                "points": 7.8,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 11,
                      "login": "niekwit"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "60 public repos, account ~8 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 60
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 8
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "moderate",
        "name": "Engineering Quality",
        "value": 60,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "at_risk",
            "name": "Engineering practices",
            "note": null,
            "notes": [],
            "value": 44,
            "inputs": {
              "has_ci": true,
              "has_tests": false,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "3 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "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": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 20,
                "status": "met",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "topics": [
                "bioinformatics-pipeline",
                "damid",
                "snakemake-workflow"
              ],
              "has_wiki": true,
              "homepage": null,
              "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": 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": "moderate",
        "name": "Security",
        "value": 53,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "packaging",
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 41,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 16,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 2,
              "scorecard_aggregate": 4.1
            },
            "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": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 0/16 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 0.8,
                "status": "partial",
                "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 0 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 not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is 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": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "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): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories",
                    "no_advisories_left_outstanding"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 2
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "source": "osv",
              "advisories": 0,
              "affected_packages": 0,
              "assessed_packages": 2,
              "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": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory 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": 2,
              "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": 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": 17,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 2,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.03,
              "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": "3 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 1.6,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 3,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "critical",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 14,
            "inputs": {
              "has_nix": false,
              "has_tests": false,
              "lockfiles": [],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "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": 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": "Dockerfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile"
                    }
                  }
                ],
                "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 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
              "primary_language": "Python",
              "largest_source_bytes": 3693,
              "source_files_sampled": 15,
              "oversized_source_files": 0
            },
            "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": "0/15 source files over 60KB",
                "points": 55,
                "status": "met",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 15,
                      "oversized": 0
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-30T20:15:58.825981Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/n/niekwit/damid-seq.svg",
  "full_name": "niekwit/damid-seq",
  "license_state": "standard",
  "license_spdx": "MIT"
}

Las puntuaciones son señales, no garantías. Reflejan prácticas públicamente visibles en GitHub; no son una auditoría de código ni una garantía de seguridad.

Los datos ausentes se excluyen y los pesos se renormalizan; nunca se puntúan como cero. La metodología es versionada y abierta: métricas v1.13.0, esquema v0.27.0 — metodología completa · wiki de métricas.

Cómo se sitúa un resultado dentro del registro general: estadísticas agregadas.