Registro público
Informe de salud del softwareesquema 0.27.0 · métricas 1.13.0 · 2026-07-28 23:42 UTC

edgardomortiz / Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

PythonGPL-3.0★ 44 estrellas⑂ 8 forksdesde jul 2020Ver en GitHub ↗

edgardomortiz/Captus tiene un índice de salud de 51 sobre 100, lo que lo sitúa en la banda Moderado. Su puntuación más alta es Vitality (86/100) y la más baja, AI Readiness (11/100). Se actualizó por última vez hace 14 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

Edgardo M. OrtizCuenta personal
84 seguidores18 repositorios públicosdesde oct 2013Florida Museum of Natural History

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?

86Excelente · 22% del índice global
Cómo se puntúa
28.8/36Recencia de push — último push hace 14 días
19.4/36Cadencia de commits — 28/52 semanas con commits
18/18Volumen de commits — 158 commits en el último año
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10
Datos de entrada utilizados
commits_last_year158
human_commit_share1
days_since_last_push14
active_weeks_last_year28
Cómo se puntúa
27/27Publica versiones — 51 versiones publicadas
36/36Recencia de las versiones — última versión hace 14 días
27/27Cadencia de publicación — una versión cada ~35 días
0/10OpenSSF Scorecard: Signed-Releases — sin datos
Datos de entrada utilizados
releases_count51
latest_release_tagv1.6.6
releases_from_tagsno
days_since_latest_release14
mean_days_between_releases35
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?

43En riesgo · 18% del índice global
Cómo se puntúa
26.5/60Estrellas — 44 estrellas
7/25Forks — 8 forks
3.9/15Observadores — 6 observadores
Datos de entrada utilizados
forks8
stars44
watchers6
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
Cómo se puntúa
22.5/22.5README
22.5/22.5Licencia — licencia reconocida (GPL-3.0)
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?

42En riesgo · 24% del índice global
Cómo se puntúa
9/54Factor bus — la mitad de los commits recae en 1 contribuyente(s)
2.4/22.5Distribución de commits — el principal contribuyente firma el 89% de los commits
4.1/13.5Amplitud de contribuyentes — 3 contribuyentes
6/10OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6
Datos de entrada utilizados
bus_factor1
contributors_sampled3
top_contributor_share0,894
Cómo se puntúa
14.9/46.8Resolución de issues — 32% de issues cerradas
38.2/38.3Aceptación de PR — 1/1 PR decididos fusionados
0/15OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0
Datos de entrada utilizados
merged_prs1
open_issues30
closed_issues14
issue_closed_ratio0,318
closed_unmerged_prs0
Cómo se puntúa
10/30Respaldo de la propiedad — cuenta personal (usuario)
0/20Dominio verificado — no aplicable a cuentas de usuario
13.9/25Alcance del propietario — 84 seguidores de edgardomortiz
21.3/25Trayectoria — 18 repos públicos, cuenta de ~12 años
Datos de entrada utilizados
followers84
owner_typeUser
is_verified
owner_loginedgardomortiz
public_repos18
account_age_days4660
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?

41En riesgo · 20% del índice global
Cómo se puntúa
0/24Flujos de trabajo de CI
0/24Pruebas presentes
0/16Configuración de linter
0/9.6Hooks de pre-commit
0/6.4.editorconfig
0/20OpenSSF Scorecard: CI-Tests — sin datos
Datos de entrada utilizados
has_cino
has_testsno
has_editorconfigno
has_linter_configno
has_precommit_configno
Excluidos de la puntuación (sin datos o no aplicable): OpenSSF Scorecard: CI-Tests. Los pesos restantes se han renormalizado.

Documentación

100Excelente
Cómo se puntúa
30/30README
25/25Directorio de documentación
15/15Sitio de documentación / página del proyecto — https://edgardomortiz.github.io/captus.docs/
10/10Descripción del repositorio
10/10Topics — 16 topics
10/10Wiki
Datos de entrada utilizados
topicsngs, phylogenomics, alignment, genome-skimming, high-throughput-sequencing, hybridization-capture, next-generation-sequencing, phylogenetics, rna-seq, whole-genome-sequencing, phylotranscriptomics, orthologs, paralogs, target-capture, bioinformatics, busco
has_wiki
homepagehttps://edgardomortiz.github.io/captus.docs/
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?

37En riesgo · 16% del índice global
Cómo se puntúa
6/7.5Binary-Artifacts — binaries present in source code
0/7.5Branch-Protection — branch protection not enabled on development/release branches
0/2.5CI-Tests — sin datos
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
1.5/2.5Contributors — project has 2 contributing companies or organizations -- score normalized to 6
0/10Dangerous-Workflow — sin datos
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 7 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — sin datos
0/5Pinned-Dependencies — sin datos
0/5SAST — no SAST tool detected
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — sin datos
0/7.5Token-Permissions — sin datos
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Datos de entrada utilizados
sourceopenssf_scorecard
checks_evaluated12
scorecard_versionv5.5.0
checks_inconclusive6
scorecard_aggregate3,7
Excluidos de la puntuación (sin datos o no aplicable): ci_tests, dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Los pesos restantes se han renormalizado.

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.

11Crítico · 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)
11.2/40Historial de commits legible — 21 de 100 commits humanos declaran su intención (asunto estructurado o cuerpo explicativo)
Datos de entrada utilizados
has_llms_txtno
legible_history_share0,21
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
0/10Entorno reproducible
0/10Práctica demostrada con agentes — ningún commit con autoría de agente entre los últimos 100
0/8Mantenimiento automatizado — no se observan actualizaciones automáticas de dependencias
0/10OpenSSF Scorecard: Pinned-Dependencies — sin datos
Datos de entrada utilizados
has_nixno
has_testsno
lockfiles
has_dockerfileno
typed_languageno
bootstrap_files
has_devcontainerno
has_linter_configno
typecheck_configs
agent_commit_share0
toolchain_manifests
dependency_bot_commit_share0
Excluidos de la puntuación (sin datos o no aplicable): OpenSSF Scorecard: Pinned-Dependencies. Los pesos restantes se han renormalizado.
Cómo se puntúa
0/45Código verificable por tipos — Python sin configuración de verificación de tipos
39.8/55Tamaños de archivo manejables — 8/29 archivos fuente de más de 60 KB
Datos de entrada utilizados
primary_languagePython
largest_source_bytes179.292
source_files_sampled29
oversized_source_files8

Datos clave

44estrellas de GitHub
3contribuidores
158commits en los últimos 12 meses
14días desde el último push
51versiones publicadas
1factor bus
30issues abiertas
PyPIecosistemas de paquetes

Advertencias de recopilación de datos

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • Could not fetch pypi package 'captus' from its registry

Más detalle

Historial de estrellas y forks 0 ★ / 8 ⇿
0Estrellas
8Forks
50Versiones

Cuándo se añadió cada estrella y fork, recopilado de GitHub y agrupado por día. El crecimiento acumulado se sitúa justo encima de las adiciones diarias que lo componen, de modo que ambos se leen en conjunto: la acumulación orgánica sostenida no se parece en nada a un pico abrupto y efímero. Cuando esa diferencia es medible, se informa como autenticidad del crecimiento.

02468812021-112024-032026-07
Mayor 1Menor 6Parche 43

Cada punto abarca 5 días.

OpenSSF Scorecard 3.7 / 10
3.7agregado

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 · 2026-07-28 23:42 UTC

8Binary-Artifactsbinaries present in source code
0Branch-Protectionbranch protection not enabled on development/release branches
n/dCI-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
6Contributorsproject has 2 contributing companies or organizations -- score normalized to 6
n/dDangerous-Workflowno workflows found
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10
n/dPackagingpackaging workflow not detected
n/dPinned-Dependenciesno dependencies found
0SASTno SAST tool detected
0Security-Policysecurity policy file not detected
n/dSigned-Releasesno releases found
n/dToken-PermissionsNo tokens found
10Vulnerabilities0 existing vulnerabilities detected
Todas las dependencias 0

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

RegistroPaqueteVersiónRelación
Avisos de dependencias sin evaluar

El cotejo de avisos no pudo ejecutarse para este informe: No resolved dependencies to assess

Informe JSON sin procesar legible por máquina
{
  "data": {
    "repo": {
      "topics": [
        "ngs",
        "phylogenomics",
        "alignment",
        "genome-skimming",
        "high-throughput-sequencing",
        "hybridization-capture",
        "next-generation-sequencing",
        "phylogenetics",
        "rna-seq",
        "whole-genome-sequencing",
        "phylotranscriptomics",
        "orthologs",
        "paralogs",
        "target-capture",
        "bioinformatics",
        "busco"
      ],
      "is_fork": false,
      "size_kb": 81629,
      "has_wiki": true,
      "homepage": "https://edgardomortiz.github.io/captus.docs/",
      "languages": {
        "Python": 1167463
      },
      "pushed_at": "2026-07-14T05:35:50Z",
      "created_at": "2020-07-16T22:37:10Z",
      "owner_type": "User",
      "updated_at": "2026-07-27T18:46:27Z",
      "description": "Assembly of Phylogenomic Datasets from High-Throughput Sequencing data",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "GPL-3.0",
      "default_branch": "master",
      "license_spdx_raw": "GPL-3.0",
      "primary_language": "Python",
      "significant_languages": [
        "Python"
      ]
    },
    "owner": {
      "blog": null,
      "name": "Edgardo M. Ortiz",
      "type": "User",
      "login": "edgardomortiz",
      "company": "Florida Museum of Natural History",
      "location": "Gainesville, Florida",
      "followers": 84,
      "avatar_url": "https://avatars.githubusercontent.com/u/5767612?v=4",
      "created_at": "2013-10-24T17:36:26Z",
      "is_verified": null,
      "public_repos": 18,
      "account_age_days": 4660
    },
    "license": {
      "state": "standard",
      "spdx_id": "GPL-3.0",
      "raw_spdx": "GPL-3.0",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [
        {
          "tag": "v1.6.6",
          "kind": "patch",
          "published_at": "2026-07-14T05:35:50Z"
        },
        {
          "tag": "v1.6.5",
          "kind": "patch",
          "published_at": "2026-02-27T20:13:42Z"
        },
        {
          "tag": "v1.6.4",
          "kind": "patch",
          "published_at": "2026-02-23T23:13:36Z"
        },
        {
          "tag": "v1.6.3",
          "kind": "patch",
          "published_at": "2026-02-22T03:04:38Z"
        },
        {
          "tag": "v1.6.2",
          "kind": "patch",
          "published_at": "2026-02-21T19:48:20Z"
        },
        {
          "tag": "v1.6.1",
          "kind": "patch",
          "published_at": "2025-11-07T23:27:18Z"
        },
        {
          "tag": "v1.6.0",
          "kind": "minor",
          "published_at": "2025-09-29T06:13:49Z"
        },
        {
          "tag": "v1.5.9",
          "kind": "patch",
          "published_at": "2025-09-12T20:39:50Z"
        },
        {
          "tag": "v1.5.8",
          "kind": "patch",
          "published_at": "2025-09-08T04:29:30Z"
        },
        {
          "tag": "v1.5.7",
          "kind": "patch",
          "published_at": "2025-09-02T07:49:16Z"
        },
        {
          "tag": "v1.5.6",
          "kind": "patch",
          "published_at": "2025-09-01T06:53:32Z"
        },
        {
          "tag": "v1.5.5",
          "kind": "patch",
          "published_at": "2025-08-28T03:55:55Z"
        },
        {
          "tag": "v1.5.4",
          "kind": "patch",
          "published_at": "2025-08-15T09:12:23Z"
        },
        {
          "tag": "v1.5.3",
          "kind": "patch",
          "published_at": "2025-08-04T21:47:11Z"
        },
        {
          "tag": "v1.5.2",
          "kind": "patch",
          "published_at": "2025-08-03T06:02:41Z"
        },
        {
          "tag": "v1.5.1",
          "kind": "patch",
          "published_at": "2025-07-15T20:48:41Z"
        },
        {
          "tag": "v1.5.0",
          "kind": "minor",
          "published_at": "2025-07-08T08:08:44Z"
        },
        {
          "tag": "v1.4.9",
          "kind": "patch",
          "published_at": "2025-07-03T04:56:54Z"
        },
        {
          "tag": "v1.4.8",
          "kind": "patch",
          "published_at": "2025-05-31T22:27:47Z"
        },
        {
          "tag": "v1.4.7",
          "kind": "patch",
          "published_at": "2025-05-26T03:30:23Z"
        },
        {
          "tag": "v1.4.6",
          "kind": "patch",
          "published_at": "2025-05-18T22:42:13Z"
        },
        {
          "tag": "v1.4.5",
          "kind": "patch",
          "published_at": "2025-05-18T05:58:31Z"
        },
        {
          "tag": "v1.4.4",
          "kind": "patch",
          "published_at": "2025-05-16T17:01:55Z"
        },
        {
          "tag": "v1.4.2",
          "kind": "patch",
          "published_at": "2025-05-13T05:09:16Z"
        },
        {
          "tag": "v1.4.1",
          "kind": "patch",
          "published_at": "2025-05-04T19:51:31Z"
        },
        {
          "tag": "v1.4.0",
          "kind": "minor",
          "published_at": "2025-04-16T17:05:38Z"
        },
        {
          "tag": "v1.3.9",
          "kind": "patch",
          "published_at": "2025-04-15T00:50:27Z"
        },
        {
          "tag": "v1.3.3",
          "kind": "patch",
          "published_at": "2025-04-09T23:22:48Z"
        },
        {
          "tag": "v1.3.2",
          "kind": "patch",
          "published_at": "2025-03-19T08:23:45Z"
        },
        {
          "tag": "v1.3.0",
          "kind": "minor",
          "published_at": "2025-03-16T06:59:38Z"
        },
        {
          "tag": "v1.2.0",
          "kind": "minor",
          "published_at": "2025-03-09T19:56:20Z"
        },
        {
          "tag": "v1.1.2",
          "kind": "patch",
          "published_at": "2025-02-24T02:21:49Z"
        },
        {
          "tag": "v1.1.1",
          "kind": "patch",
          "published_at": "2025-01-29T02:52:59Z"
        },
        {
          "tag": "v1.1.0",
          "kind": "minor",
          "published_at": "2024-12-23T17:49:26Z"
        },
        {
          "tag": "v1.0.1",
          "kind": "patch",
          "published_at": "2024-03-02T19:48:29Z"
        },
        {
          "tag": "v1.0.0",
          "kind": "major",
          "published_at": "2023-11-21T10:57:05Z"
        },
        {
          "tag": "v0.9.99",
          "kind": "patch",
          "published_at": "2023-11-14T15:47:27Z"
        },
        {
          "tag": "v0.9.98",
          "kind": "patch",
          "published_at": "2023-10-30T11:03:57Z"
        },
        {
          "tag": "v0.9.97",
          "kind": "patch",
          "published_at": "2023-09-02T13:56:17Z"
        },
        {
          "tag": "v0.9.96",
          "kind": "patch",
          "published_at": "2023-08-25T14:57:30Z"
        },
        {
          "tag": "v0.9.95",
          "kind": "patch",
          "published_at": "2023-08-18T14:52:11Z"
        },
        {
          "tag": "v0.9.93",
          "kind": "patch",
          "published_at": "2023-06-08T05:49:14Z"
        },
        {
          "tag": "v0.9.92",
          "kind": "patch",
          "published_at": "2023-05-26T08:52:21Z"
        },
        {
          "tag": "v0.9.91",
          "kind": "patch",
          "published_at": "2022-12-29T15:52:28Z"
        },
        {
          "tag": "v0.9.90",
          "kind": "patch",
          "published_at": "2022-12-13T23:34:10Z"
        },
        {
          "tag": "v0.9.89",
          "kind": "patch",
          "published_at": "2022-11-27T21:32:48Z"
        },
        {
          "tag": "v0.9.88",
          "kind": "patch",
          "published_at": "2022-11-11T12:51:26Z"
        },
        {
          "tag": "v0.9.86",
          "kind": "patch",
          "published_at": "2022-07-21T07:14:19Z"
        },
        {
          "tag": "v0.9.85",
          "kind": "patch",
          "published_at": "2022-07-19T11:00:06Z"
        },
        {
          "tag": "v0.9.84",
          "kind": "patch",
          "published_at": "2022-07-12T12:30:09Z"
        },
        {
          "tag": "v0.9.83",
          "kind": "patch",
          "published_at": "2022-07-10T22:04:13Z"
        }
      ],
      "recent_commits": [
        {
          "oid": "7d991867363e701e8e7a1ddf1f43848ffef536d8",
          "body": null,
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-07-14T04:52:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b89a15ce37981e6eb2da569850f057e630047fc8",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-07-13T05:44:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f6de9c8e88c3b301f8f53feaca6fef0ddfbd30c8",
          "body": "Added `--ram` option to `new_targets_from_alignments` to limit the max amount of RAM for mmseqs",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-07-13T05:37:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b8283760428e1a679b700247773e03c9237d7104",
          "body": null,
          "is_bot": false,
          "headline": "Change cluster-mode to 2 as default all across",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-23T06:21:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8fcd46fa301fb0f53fd5bc3560120506ef31fe43",
          "body": null,
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-13T04:41:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9e2358e9e2b4441abcbae037bc97f67ce146b929",
          "body": null,
          "is_bot": false,
          "headline": "Update settings.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-09T04:48:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bde3a2db2b7f423f96244ea66c0c9bd0b4587f77",
          "body": "Fix `ctg_mean_depth` formatting",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-09T04:31:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "34692c0c076b8c182c48e65b86997003b402fe1f",
          "body": null,
          "is_bot": false,
          "headline": "Update captus_design.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-09T00:44:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8a72672d744d322b53300da967919cc0e975bf7f",
          "body": "Cover the case of empty lines in path lists",
          "is_bot": false,
          "headline": "Improved list consumption",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-06-08T16:13:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "484afd4c341f1aa6485c237844e7ae0a758e398c",
          "body": "- Changed defaults",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-28T02:29:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec62d21403385d073045610da8f823528c968eff",
          "body": null,
          "is_bot": false,
          "headline": "Change coverage defaults",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-23T04:51:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "af9f667e70b2501c8246279bf2527eda6efbd269",
          "body": null,
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-22T18:52:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "908c0f90858a686b27942289bf411ccdb2360279",
          "body": "-Simply quit if extractions directory(ies) is/are not found",
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-22T18:50:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6e5d32b8aa33212238ee3e2768f15e417a85904d",
          "body": "Fixed warning about missing `captus-extract_refs.json` file",
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-22T18:42:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f6256ec279370be419526e072b61b524ce04acd7",
          "body": "- Exposed MMseqs' `cluster_mode` and `cov_mode` as additional options for `new_targets_from_alignments`, defaults are still `cluster_mode 2` and `cov_mode 1`.",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-22T15:30:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8ca739fef0c86354e6b71de009a0ebf5547a15cc",
          "body": "- Last change of defaults for W and C from 0.6666 to 0.3333",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-21T21:16:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "362f1658bec35ed4b4b786b7e96fb8324163d388",
          "body": "- Fixed hover menu for sample-wise stats",
          "is_bot": false,
          "headline": "Update report.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-21T20:25:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6a5a312f08ff0f505352d4bc1e2e483f1e4906d6",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-21T02:26:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "17983aef3908a5961660aee90c8cadd0aa2b97a1",
          "body": "- Improved logic for paralog splitting, now PMIN is only added when its total sample proportion is equal or exceeds `min_sample_prop`",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-21T02:13:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "84fe98210cdcbe25c686e9cd852e11dac37ff975",
          "body": null,
          "is_bot": false,
          "headline": "Updated in-run explanations",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-15T10:28:59Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fa26a8b7730a23338f9d1a2eae5e7fadf6f70c51",
          "body": "Another fix for reclustering",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-14T17:28:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "00cb0e9be6746c5fa827caef989b172fadae2838",
          "body": "Additional fixes to last commit, the reclustering process matches more closely the logic of `new_targets_from_alignments`",
          "is_bot": false,
          "headline": "Updated extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-14T16:36:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "78aa5eab81a455048d8621c1ecefdba8998f410d",
          "body": "Another fix",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-13T22:49:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7cca7151a175cda94efdcf8eafb02908b5bb78d9",
          "body": "Linked to last commit",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-13T22:29:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c8abafb311ec24ffeb31082d5345d33ef5e5a0aa",
          "body": "After reclustering representatives a second check for `min_samples` and `max_copies` must be done",
          "is_bot": false,
          "headline": "Fixed reclustering of representatives in `captus extract`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-13T22:21:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0670d79a9a20fa4da08be3d189b176b68f0e24c",
          "body": null,
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T13:39:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0cf1de386a9427a20ca87389200db6ea581f4ac4",
          "body": "Sync variables and drop down menus",
          "is_bot": false,
          "headline": "Update report.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T12:53:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4c052921e14aed3290d2f0bcd521096f0917751f",
          "body": "Update function after switching to median for copies",
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T12:24:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9fe104592ad9a8bf38a3bc38ce2da818f77d30d3",
          "body": null,
          "is_bot": false,
          "headline": "Ruff run",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T11:34:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cbf0ba255dfdf33e8eb315fca2af9b7569727bdc",
          "body": "Round `ctg_mean_depth` to 4 decimals",
          "is_bot": false,
          "headline": "Update bioformats.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T09:14:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3a5163faf63e494edcf17fccfda818e06a252b3b",
          "body": "Round `ctg_mean_depth` to 4 decimals",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T09:09:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ca7623431edac16878e52cad8573a96c3ac9c298",
          "body": "- `captus align` report median and mean copies\n- Rename column names from avg_ to mean_\n- Rename option `align_min_species` to `clust_min_species`, added option `align_min_samples` to `captusd cluster`\n- Added options `median_copies` and `mean_copies` to `captusd select`\n- Updated all relevant report (review required)",
          "is_bot": false,
          "headline": "Preferred use of median copies instead of mean",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-11T08:44:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d1c36b17e7c0684a05a2ffd92d1b83023fb70759",
          "body": "- Expanded description for warnings about bugs in some dependencies",
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-07T13:12:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5311062e4f0a2551bd05ac238fbc56ea99555b5e",
          "body": "This belongs to previous commit too",
          "is_bot": false,
          "headline": "Improved `redo_from` in `captus align`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-07T08:34:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9b008402c6354dd0f36607f97724e41276dfbd78",
          "body": "The deletion of folder before redoing steps is now more granular and obeys changes in `markers` and `formats`. For example, an initial set of settings can be used to trim all formats (AA,NT,GE) but then setting can be changed and run with `redo_from` only for GE for example.",
          "is_bot": false,
          "headline": "Improved `redo_from` in `captus align`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-07T08:33:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5bd8c25c5c2d1ab3ae468768cc9b0acc572e5f6e",
          "body": "Updated preprint title",
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-06T14:15:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4ccc1f2bfe8d3a845cda7147edcd33aeee84d3f9",
          "body": "- Use the median number of sequences per sample in a cluster instead of the average (missed file in last commit)",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-02T17:20:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "99d5dadf2a0b3fe73ecbaf6f2be0a0c629fdf3ef",
          "body": "- Use the median number of sequences per sample in a cluster instead of the average",
          "is_bot": false,
          "headline": "`cl_max_copies` is now median",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-02T17:16:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9cbf53ff59531c0f7a1c305e02b15f72f9b58865",
          "body": "Cosmetic changes",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T17:21:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0483967f2b5dfce0cb80f5b99b2a2ded32885d34",
          "body": "- Don't overcount split paralogs",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T16:12:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "30fcf802910440349c83f970bc57d857a701f960",
          "body": "Using median copies, changed defaults",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T05:33:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e99404b0c7aabca40f9a49bf02f410d18d1e4366",
          "body": "- Switch to using median copies instead of average copies",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T04:51:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3402186bb3c98b2763da6b689524c886cbead189",
          "body": "Fixing the logic of paralog-splitting",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T03:14:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e39aff0600ea3321a1d6c4cc49746f446c2d4b2f",
          "body": "- Add 'low_copy_only' too",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T02:38:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "51c99f68d594ea7ada57270604ba9d7567639198",
          "body": "- Add option to remove low copy loci, useful for optimizing paralog-splitting parameters",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-05-01T02:31:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "aadb6ced77fcffc2afb7d90fb40a2638df73d600",
          "body": "- Changed default of `min_depth_proportion` from 0.55 to 0.33",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-30T18:39:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2555078c9f5fc9b18b693b2f87f934e87d7552cd",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T20:11:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "43ff43cb422a294614e7e6d41d77147eed8b16e4",
          "body": "- Calculate 'sample_pct' even when not splitting paralogs",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T20:07:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "965c8fde9fdd456378a9f8a8f27f75bed465f37c",
          "body": "Remove empty alignment columns after removing reference target sequences",
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T15:29:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9200d2ece2fd33ce88b32c69b4e81a106a474f53",
          "body": null,
          "is_bot": false,
          "headline": "Locate refs.json automatically if possible",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T08:46:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6e4d09266f7798197e261ed01d4d7151fe5f0b07",
          "body": null,
          "is_bot": false,
          "headline": "Update captus_assembly.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T07:47:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c1e765cf8f9084c47caf2234d3600f81db778dbe",
          "body": "`--cl_max_copies` changed to 3 from 6, this means every sample is allowed to have at most 3 sequences in a cluster, increase if your assemblies are highly fragmented, in a cluster an extra sequence doesn't become an additional copy directly and instead could be a non-overlapping fragment.",
          "is_bot": false,
          "headline": "Default change",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-29T05:41:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5915638caa727d1adf4043eb490ee79afe3f11d6",
          "body": "- Rename PAR0 to PMIN to indicate a paralog composed of minor alleles",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-28T21:43:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "66078cfeb7c12408aa23e6b55b2e81984ca65163",
          "body": "Changed some defaults",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-28T18:43:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bbd321ec88e2eec8988725582534130dc0b7b731",
          "body": "- Added per target info (% samples in locus retained, copies)",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-28T18:38:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "289bbfdb23a8bd2df8c9612b142d9df0c781cfd4",
          "body": null,
          "is_bot": false,
          "headline": "Minor fixes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-27T19:31:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3c3672f04366e626101a7dadee163e9199e9fc6f",
          "body": "- Sanitize sequence names during importation, replace `:`, `(`, or `)` with `_`",
          "is_bot": false,
          "headline": "Sanitize sequence names",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-27T06:25:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "40f1e7c0b7ce3627981ec93c63ec447c1b298e60",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-27T01:45:19Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d39860e163c9c58ffd0a510b5787c2c1a2dac6e7",
          "body": "Cosmetic changes",
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-26T21:55:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "11b3ac8accf7f8071254d5ea5b268091337c443f",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-26T20:32:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3a5d8a5aa9af636f4628eafbd46ad3f54ed124f5",
          "body": "- Save an additional table with run statistics for easy concatenation across several runs",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-26T18:54:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "14653364b9d147e600b7c94d6a64057ff939f8ee",
          "body": "- Added `--retain_samples` to retain a list of samples even if the don't pass the `--min_depth_proportion` threshold, useful if a small group of sequences is very divergent and consistently produces small clusters, like for example in the case of an outgroup",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-26T17:51:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e4e17c625f33381d11419bb7dfb600e4583ae0c3",
          "body": null,
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-25T05:00:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b37526f8c9a456d34e7c93d1dfebc150f86430be",
          "body": "- Show assembly and extraction directories not found",
          "is_bot": false,
          "headline": "Update extract.py and align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-25T04:58:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "70529e63703b3b3a201600fe575441bd97eea4ab",
          "body": "Improved explanations",
          "is_bot": false,
          "headline": "Cosmetic changes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-24T06:45:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "33f0bb4206b23a6466bb67d2ff0010f6f15eba17",
          "body": null,
          "is_bot": false,
          "headline": "Cosmetic changes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-24T06:07:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "791d2710892f005f8263b83ca8530e73af5991b5",
          "body": "- You can use a list of paths to individual sample extraction folders (ending in __captus-ext) to `captus align`. Useful when your extractions are in separate captus extractions folders or just need align subsets of samples\n- The name in symbolic links are honored",
          "is_bot": false,
          "headline": "List of paths allowed in `captus align`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-24T05:53:59Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "485e8074965fb969ab604a361139994aa145ff50",
          "body": "- You can use a list of paths to individual sample assembly folders (ending in __captus-asm) to `captus extract`. Useful when your assemblies are in separate captus assembly folders\n- The name in symbolic links are honored\n- Reduced default `--min_coverage` to 0.2 in `captus align`",
          "is_bot": false,
          "headline": "Lists of paths allowed in `captus extract`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-24T03:58:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cdfe144e574949d036bd616e34c5f0cfab138309",
          "body": null,
          "is_bot": false,
          "headline": "Update settings.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-21T21:59:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "821c598c5c91cdb628406a3fbfa8d6dd2c5c64aa",
          "body": "- Added `--min_length` to `captus clean`\n- Added new ClipKIT's modes to Captus' choices (`gappyout`, `block-gappy`, `composition-bias`, `heterotachy`)",
          "is_bot": false,
          "headline": "Added options",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-21T21:38:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a8456da485e79f416f84f3f28894516a2dc4b455",
          "body": "- Fixed a bug caused by comparing versions as decimal numbers",
          "is_bot": false,
          "headline": "Check minimum versions correctly",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-21T17:04:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "680ecd96199efe1adebfa8a89f0240970b813ce2",
          "body": null,
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-20T07:56:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "015bd65360c929a92ac9a81f60ae8674e10c959c",
          "body": null,
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-20T07:53:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7740fb669df5176aae215c885fd9d10d25858ad3",
          "body": "Skip alignment of loci with many copies",
          "is_bot": false,
          "headline": "Added `max_average_copies` to `captus align`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-20T07:50:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ea928252ff5ff0ae504a59e97ff8dbd742c4e8b4",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-19T22:35:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e9ec187c5f3a04db110fa436a8c82c25e4cc158c",
          "body": null,
          "is_bot": false,
          "headline": "Bug fixes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-19T18:05:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9b636f712b3fbeb935e2e3ea4b374e230ebe6a45",
          "body": "- Changed query= to target= in output sequences",
          "is_bot": false,
          "headline": "Cosmetic changes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-19T01:33:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e9c32f63b0bb054c5991392fcd4996e5ccd22d30",
          "body": "- Add a cleanup for IQ-TREE output files\n- Fixed bug in `new_targets_from_alignments`",
          "is_bot": false,
          "headline": "IQ-TREE cleanup",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T22:23:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1e9e69af7cb6c5e6903be56f02350de2c95338c0",
          "body": null,
          "is_bot": false,
          "headline": "Update copyright date",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T07:37:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5103798a5596f23a07dec0b7fcf19dbf8aee0d22",
          "body": "Help is shown if no options are provided",
          "is_bot": false,
          "headline": "Improved accessory scripts",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T07:28:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7b84ea47bde34deb47f824b54c65006f69fef565",
          "body": null,
          "is_bot": false,
          "headline": "Allow symbolic links to import assemblies",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T07:24:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "47a8006d72861b32d628f093441e8d3268399a30",
          "body": "Also allow symbolic links for imported FASTA assemblies",
          "is_bot": false,
          "headline": "Tidy up `phylo_commands`",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T06:51:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d9f407a3fa52c4e11035a308b1667e89fc53da9e",
          "body": "Fixed message about skipped empty/corrupt FASTQs",
          "is_bot": false,
          "headline": "Update assemble.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-18T05:05:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d0b1d21b44ec12ddcb7b2fa9f0979eea4ce3f5d6",
          "body": null,
          "is_bot": false,
          "headline": "Update extract.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-17T23:36:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "be2d10447e4718b316948856bbf2775fc350a50a",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-17T17:15:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6ab1fb538ff6e649a7c9b919d6eba309ca31e5a7",
          "body": "- New default `cl_mode` for `captus extract` is 1, new `cl_min_coverage` is 50, relaxed `cl_max_copies` to 6",
          "is_bot": false,
          "headline": "Changed clustering defaults",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-17T16:56:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a8bff1f04e82a0e9fc8e23f4cb5bebb6c6e712de",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-17T14:27:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c0e959db158a5ea379a1196601ac90904b1c339e",
          "body": null,
          "is_bot": false,
          "headline": "Warning messages for empty FASTQs",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-17T04:06:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "867acc62aaba0333b6b2acb35b977a8d526ed2b0",
          "body": null,
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-16T21:06:09Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "998d2b96908d16639cead88868b059786be4f784",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-16T16:52:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6ccbeb1f1d75768cc0c72019af746df2e30f13a8",
          "body": null,
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-16T06:12:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "40a82d9be1a1f8429626bed97be20acafbfd0288",
          "body": "Add warnings about buggy versions",
          "is_bot": false,
          "headline": "Update README.md",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-16T03:02:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "027e7305da66b7af94bc0984667fd2ccc1472cb0",
          "body": "Additional bug fixes",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-16T02:40:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "46770a55e84d21e09e881380d7e8842083a0f166",
          "body": "Small bug fixes",
          "is_bot": false,
          "headline": "Update new_targets_from_alignments.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-15T20:07:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "530e452ce2dc861278e8f04589f16b4ab8a2429b",
          "body": "- Added empty/corrupted file check for FASTQs\n- Added `sample_bases_target` to `captus assemble`\n- Added value check for paralog tolerances parameters (transform percentages to proportions automatically)\n- Improvements to `phylo_commands`, added some IQTREE options\n- Changed minimum read length from\n[…]\nlt Salmon kmer size for indexing\n- `new_targets_from_alignments` has been completely rewritten, workflow is better explained during execution, it can auto-split paralogous loci into new separate loci.",
          "is_bot": false,
          "headline": "Updating to v1.6.6",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-04-15T17:32:35Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "73290b4a0d83fc5e87a3f765adc5611bf25a1c87",
          "body": "- Fix for `min_data_per_column`, sometimes the percentage didn't remove the exact number of columns expected because of a rounding error.",
          "is_bot": false,
          "headline": "Minor fixes",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-03-27T06:29:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f197f38b97b1efa60a684cfa007060afd8474075",
          "body": "- Baits are created faster, less to deduplicate.\n- RAM and CPUs better assigned during loci extraction.",
          "is_bot": false,
          "headline": "Optimization and speedups",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-03-19T18:15:23Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4b6396824ac4b3bdf65d3eacfe4d2f0ff6503466",
          "body": null,
          "is_bot": false,
          "headline": "Changed hit region determination formula",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-03-03T05:59:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e6afee88d33506c8e263d1caaf3aa175c03cb021",
          "body": "Fix directories dictionaries",
          "is_bot": false,
          "headline": "Update align.py",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-03-01T18:09:23Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "caaecd2f43a5a31312b165c85470685201e15fa1",
          "body": "The function to find FASTAs now takes into account MARKER and FORMAT",
          "is_bot": false,
          "headline": "Granular selection of alignments",
          "author_name": "Edgardo M. Ortiz",
          "author_login": "edgardomortiz",
          "committed_at": "2026-03-01T18:04:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        }
      ],
      "releases_count": 51,
      "commits_last_year": 158,
      "latest_release_at": "2026-07-14T05:35:50Z",
      "latest_release_tag": "v1.6.6",
      "releases_from_tags": false,
      "days_since_last_push": 14,
      "active_weeks_last_year": 28,
      "days_since_latest_release": 14,
      "mean_days_between_releases": 35
    },
    "community": {
      "has_readme": true,
      "has_license": true,
      "has_description": true,
      "has_contributing": false,
      "health_percentage": 42,
      "has_issue_template": false,
      "has_code_of_conduct": false,
      "has_pull_request_template": false
    },
    "ecosystem": {
      "packages": []
    },
    "popularity": {
      "forks": 8,
      "stars": 44,
      "watchers": 6,
      "fork_history": {
        "days": [
          {
            "date": "2021-11-06",
            "count": 1
          },
          {
            "date": "2022-02-28",
            "count": 1
          },
          {
            "date": "2022-07-11",
            "count": 1
          },
          {
            "date": "2023-05-18",
            "count": 1
          },
          {
            "date": "2023-08-09",
            "count": 1
          },
          {
            "date": "2025-03-13",
            "count": 1
          },
          {
            "date": "2025-10-13",
            "count": 1
          },
          {
            "date": "2026-07-14",
            "count": 1
          }
        ],
        "complete": true,
        "collected": 8,
        "total_forks": 8
      },
      "star_history": null,
      "open_issues_and_prs": 30
    },
    "ai_readiness": {
      "has_nix": false,
      "example_dirs": [],
      "has_llms_txt": false,
      "has_dockerfile": false,
      "has_mcp_signal": false,
      "bootstrap_files": [],
      "api_schema_files": [],
      "has_devcontainer": false,
      "typecheck_configs": [],
      "toolchain_manifests": [],
      "largest_source_bytes": 179292,
      "source_files_sampled": 29,
      "oversized_source_files": 8,
      "agent_instruction_files": [],
      "agent_instruction_max_bytes": null
    },
    "dependencies": {
      "manifests": [
        "setup.py"
      ],
      "advisories": {
        "error": "No resolved dependencies to assess",
        "scope": "repository_graph",
        "source": null,
        "findings": [],
        "collected": false,
        "malicious": [],
        "truncated": false,
        "by_severity": {},
        "advisory_count": 0,
        "affected_count": 0,
        "assessed_count": 0,
        "malicious_count": 0,
        "assessed_package": null,
        "unassessed_count": 0,
        "direct_affected_count": 0
      },
      "ecosystems": [
        "pypi"
      ],
      "dependencies": [],
      "all_dependencies": {
        "error": null,
        "source": "github-sbom",
        "packages": [],
        "collected": true,
        "truncated": false,
        "total_count": 0,
        "direct_count": 0,
        "indirect_count": 0
      }
    },
    "maintainership": {
      "issues": {
        "open_prs": 0,
        "merged_prs": 1,
        "open_issues": 30,
        "closed_ratio": 0.318,
        "closed_issues": 14,
        "closed_unmerged_prs": 0
      },
      "bus_factor": 1,
      "bot_contributors": 0,
      "top_contributors": [
        {
          "type": "User",
          "login": "edgardomortiz",
          "commits": 551,
          "avatar_url": "https://avatars.githubusercontent.com/u/5767612?v=4"
        },
        {
          "type": "User",
          "login": "shigita",
          "commits": 63,
          "avatar_url": "https://avatars.githubusercontent.com/u/40628880?v=4"
        },
        {
          "type": "User",
          "login": "SethMusker",
          "commits": 2,
          "avatar_url": "https://avatars.githubusercontent.com/u/16952350?v=4"
        }
      ],
      "contributors_sampled": 3,
      "top_contributor_share": 0.894
    },
    "quality_signals": {
      "has_ci": false,
      "has_tests": false,
      "ci_workflows": [],
      "has_docs_dir": true,
      "linter_configs": [],
      "has_editorconfig": false,
      "has_linter_config": false,
      "has_precommit_config": false
    },
    "security_signals": {
      "lockfiles": [],
      "scorecard": {
        "checks": [
          {
            "name": "Binary-Artifacts",
            "score": 8,
            "reason": "binaries present in source code",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
          },
          {
            "name": "Branch-Protection",
            "score": 0,
            "reason": "branch protection not enabled on development/release branches",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
          },
          {
            "name": "CI-Tests",
            "score": null,
            "reason": "no pull request found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
          },
          {
            "name": "CII-Best-Practices",
            "score": 0,
            "reason": "no effort to earn an OpenSSF best practices badge detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
          },
          {
            "name": "Code-Review",
            "score": 0,
            "reason": "Found 0/30 approved changesets -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 6,
            "reason": "project has 2 contributing companies or organizations -- score normalized to 6",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": null,
            "reason": "no workflows found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
          {
            "name": "Dependency-Update-Tool",
            "score": 0,
            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
          },
          {
            "name": "Fuzzing",
            "score": 0,
            "reason": "project is not fuzzed",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
          },
          {
            "name": "License",
            "score": 10,
            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
          },
          {
            "name": "Maintained",
            "score": 10,
            "reason": "30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
          },
          {
            "name": "Packaging",
            "score": null,
            "reason": "packaging workflow not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
          },
          {
            "name": "Pinned-Dependencies",
            "score": null,
            "reason": "no dependencies found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "no SAST tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
          },
          {
            "name": "Security-Policy",
            "score": 0,
            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
          },
          {
            "name": "Signed-Releases",
            "score": null,
            "reason": "no releases found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
          },
          {
            "name": "Token-Permissions",
            "score": null,
            "reason": "No tokens found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
          {
            "name": "Vulnerabilities",
            "score": 10,
            "reason": "0 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
          }
        ],
        "commit": "7d991867363e701e8e7a1ddf1f43848ffef536d8",
        "ran_at": "2026-07-28T23:42:23Z",
        "aggregate_score": 3.7,
        "scorecard_version": "v5.5.0"
      },
      "has_codeql_workflow": false,
      "has_security_policy": false,
      "has_dependabot_config": false
    },
    "contribution_flow": {
      "collected": true,
      "ci_last_run_at": null,
      "oldest_open_prs": [],
      "last_merged_pr_at": "2023-06-09T15:17:07Z",
      "ci_last_conclusion": null,
      "oldest_open_issues": [
        {
          "number": 1,
          "created_at": "2023-02-22T19:35:56Z",
          "last_comment_at": "2023-02-23T15:27:54Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 3,
          "created_at": "2023-06-01T21:44:48Z",
          "last_comment_at": "2023-06-06T07:56:25Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 4,
          "created_at": "2023-11-24T06:56:37Z",
          "last_comment_at": "2023-12-05T05:21:08Z",
          "last_comment_author": "korjent"
        },
        {
          "number": 5,
          "created_at": "2024-01-29T00:55:29Z",
          "last_comment_at": "2024-03-04T20:48:27Z",
          "last_comment_author": "EdBiffin"
        },
        {
          "number": 6,
          "created_at": "2024-02-29T15:20:46Z",
          "last_comment_at": "2024-02-29T16:41:38Z",
          "last_comment_author": "veronicamb"
        },
        {
          "number": 8,
          "created_at": "2024-04-03T09:19:35Z",
          "last_comment_at": "2024-04-05T11:41:24Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 10,
          "created_at": "2024-05-14T12:54:42Z",
          "last_comment_at": "2024-08-20T04:02:54Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 12,
          "created_at": "2024-06-28T00:53:35Z",
          "last_comment_at": "2024-08-05T23:12:40Z",
          "last_comment_author": "EdBiffin"
        },
        {
          "number": 13,
          "created_at": "2024-06-28T18:23:51Z",
          "last_comment_at": "2024-09-24T03:51:54Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 14,
          "created_at": "2024-09-02T15:31:19Z",
          "last_comment_at": "2025-04-01T18:32:43Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 15,
          "created_at": "2024-09-21T14:58:18Z",
          "last_comment_at": "2024-09-28T11:08:44Z",
          "last_comment_author": "Kailin-Sun"
        },
        {
          "number": 20,
          "created_at": "2025-01-15T11:13:53Z",
          "last_comment_at": "2025-02-17T11:55:03Z",
          "last_comment_author": "vincianem"
        },
        {
          "number": 22,
          "created_at": "2025-04-01T15:37:40Z",
          "last_comment_at": "2025-04-01T15:42:31Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 24,
          "created_at": "2025-05-01T20:29:09Z",
          "last_comment_at": "2025-05-05T16:10:59Z",
          "last_comment_author": "CaroSci"
        },
        {
          "number": 25,
          "created_at": "2025-05-13T09:10:20Z",
          "last_comment_at": "2025-05-21T01:54:08Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 26,
          "created_at": "2025-05-14T15:02:55Z",
          "last_comment_at": "2025-09-18T15:38:08Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 29,
          "created_at": "2025-07-24T17:35:00Z",
          "last_comment_at": "2026-05-01T20:31:31Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 30,
          "created_at": "2025-08-11T18:21:54Z",
          "last_comment_at": "2025-08-12T16:10:07Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 31,
          "created_at": "2025-10-06T15:19:16Z",
          "last_comment_at": "2025-10-09T17:03:19Z",
          "last_comment_author": "edgardomortiz"
        },
        {
          "number": 32,
          "created_at": "2025-10-10T00:58:15Z",
          "last_comment_at": "2025-10-22T17:49:41Z",
          "last_comment_author": "edgardomortiz"
        }
      ]
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/edgardomortiz/Captus",
    "host": "github.com",
    "name": "Captus",
    "owner": "edgardomortiz"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "moderate",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 51,
      "inputs": {
        "security": 37,
        "vitality": 86,
        "community": 43,
        "governance": 42,
        "engineering": 41
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "excellent",
        "name": "Vitality",
        "value": 86,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "good",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 76,
            "inputs": {
              "commits_last_year": 158,
              "human_commit_share": 1,
              "days_since_last_push": 14,
              "active_weeks_last_year": 28
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 14 days ago",
                "points": 28.8,
                "status": "partial",
                "details": [
                  {
                    "code": "push_recency",
                    "params": {
                      "days": 14
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "28/52 weeks with commits",
                "points": 19.4,
                "status": "partial",
                "details": [
                  {
                    "code": "commit_cadence_weeks",
                    "params": {
                      "weeks": 28
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "158 commits in the last year",
                "points": 18,
                "status": "met",
                "details": [
                  {
                    "code": "commits_last_year",
                    "params": {
                      "count": 158
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "release_discipline",
            "band": "excellent",
            "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": 100,
            "inputs": {
              "releases_count": 51,
              "latest_release_tag": "v1.6.6",
              "releases_from_tags": false,
              "days_since_latest_release": 14,
              "mean_days_between_releases": 35
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "51 releases published",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "releases_published",
                    "params": {
                      "count": 51
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "latest release 14 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "release_recency",
                    "params": {
                      "days": 14
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "a release every ~35 days",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "release_cadence",
                    "params": {
                      "gap": 35
                    }
                  }
                ],
                "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": 14,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 14 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 14
                    }
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "at_risk",
        "name": "Community & Adoption",
        "value": 43,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "at_risk",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 37,
            "inputs": {
              "forks": 8,
              "stars": 44,
              "watchers": 6,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "44 stars",
                "points": 26.5,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 44
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "8 forks",
                "points": 7,
                "status": "partial",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 8
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "6 watchers",
                "points": 3.9,
                "status": "partial",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 6
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "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 (GPL-3.0)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "GPL-3.0"
                    }
                  }
                ],
                "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": 42,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "critical",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 22,
            "inputs": {
              "bus_factor": 1,
              "contributors_sampled": 3,
              "top_contributor_share": 0.894
            },
            "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 89% of commits",
                "points": 2.4,
                "status": "partial",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 89
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "3 contributors",
                "points": 4.1,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 2 contributing companies or organizations -- score normalized to 6",
                "points": 6,
                "status": "partial",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "moderate",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 53,
            "inputs": {
              "merged_prs": 1,
              "open_issues": 30,
              "closed_issues": 14,
              "issue_closed_ratio": 0.318,
              "closed_unmerged_prs": 0
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "32% of issues closed",
                "points": 14.9,
                "status": "partial",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 32
                    }
                  }
                ],
                "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 0/30 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": 56,
            "inputs": {
              "followers": 84,
              "owner_type": "User",
              "is_verified": null,
              "owner_login": "edgardomortiz",
              "public_repos": 18,
              "account_age_days": 4660
            },
            "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": "84 followers of edgardomortiz",
                "points": 13.9,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 84,
                      "login": "edgardomortiz"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "18 public repos, account ~12 yr old",
                "points": 21.3,
                "status": "partial",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 18
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 12
                    }
                  }
                ],
                "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": 41,
        "weight": 0.2,
        "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": {}
              }
            ],
            "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": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "topics": [
                "ngs",
                "phylogenomics",
                "alignment",
                "genome-skimming",
                "high-throughput-sequencing",
                "hybridization-capture",
                "next-generation-sequencing",
                "phylogenetics",
                "rna-seq",
                "whole-genome-sequencing",
                "phylotranscriptomics",
                "orthologs",
                "paralogs",
                "target-capture",
                "bioinformatics",
                "busco"
              ],
              "has_wiki": true,
              "homepage": "https://edgardomortiz.github.io/captus.docs/",
              "has_readme": true,
              "has_docs_dir": true,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 25,
                "status": "met",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": "https://edgardomortiz.github.io/captus.docs/",
                "points": 15,
                "status": "met",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "16 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 16
                    }
                  }
                ],
                "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": 37,
        "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": 37,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 12,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 6,
              "scorecard_aggregate": 3.7
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "binaries present in source code",
                "points": 6,
                "status": "partial",
                "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 2 contributing companies or organizations -- score normalized to 6",
                "points": 1.5,
                "status": "partial",
                "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": "30 commit(s) and 7 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": "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": "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": 3
            },
            "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": 11,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 11,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.21,
              "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": "21 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 11.2,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 21,
                      "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": "at_risk",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "primary_language": "Python",
              "largest_source_bytes": 179292,
              "source_files_sampled": 29,
              "oversized_source_files": 8
            },
            "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": "8/29 source files over 60KB",
                "points": 39.8,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 29,
                      "oversized": 8
                    }
                  }
                ],
                "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",
    "Could not fetch pypi package 'captus' from its registry"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-28T23:42:33.522561Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/e/edgardomortiz/Captus.svg",
  "full_name": "edgardomortiz/Captus",
  "license_state": "standard",
  "license_spdx": "GPL-3.0"
}

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.