公开记录
软件健康报告模式 0.27.0 · 指标 1.13.0 · 2026-07-28 23:42 UTC

edgardomortiz / Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

PythonGPL-3.0★ 44 星标⑂ 8 复刻始于 2020年7月在 GitHub 上查看 ↗

edgardomortiz/Captus 的健康指数为 100 分中的 51 分,处于「中等」区间。 其得分最高的类别是Vitality(86/100),最低的是AI Readiness(11/100)。 最近一次更新在 14 天前。 近期的大部分工作由 1 位贡献者完成。

51
总分 / 100
中等

软件健康指数

指标归入加权类别,统一采用 1–100 量表。总体分先取类别加权平均;当公开证据触发高风险司法辖区政策时,评级会按政策调整,并设置 49(有风险)的上限。AI 就绪度不计入总体分。

51
优秀85-100堪称典范;基本满足所有检验标准
良好70-84健康;仅有轻微不足
中等50-69可接受,但存在明显不足;建议进行审查
存在风险30-49存在重大薄弱环节;采用时应保持审慎
危急1-29问题严重(项目被弃置、仅有单一维护者、缺乏基本工程规范)
活力社区与采用可持续性与治理工程质量安全AI 就绪度

评分画像

每条轴代表一个类别。形状比平均值更重要——健康的对象会填满整个图形,而“一峰一谷”式画像意味着某一维度的优势正掩盖另一维度的风险。

所有权

Edgardo M. Ortiz个人账户
84 关注者18 个公开仓库始于 2013年10月Florida Museum of Natural History

该仓库由个人账户拥有。相较于组织支持的项目,单一所有者项目的延续性风险更高。

按类别列示的指标

活力

项目是否仍有生命——是否仍在编写代码,是否仍在发布版本?

86优秀 · 占总体的 22%
评分方式
28.8/36推送新近度 — 最近一次推送于 14 天前
19.4/36提交节奏 — 52 周中有 28 周有提交
18/18提交量 — 最近一年 158 次提交
10/10OpenSSF Scorecard:Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10
所用输入
commits_last_year158
human_commit_share1
days_since_last_push14
active_weeks_last_year28

发布纪律

100优秀
评分方式
27/27有发布版本 — 已发布 51 个发布版本
36/36发布时效 — 最近一次发布版本于 14 天前
27/27发布节奏 — 约每 35 天发布一次
0/10OpenSSF Scorecard:Signed-Releases — 无数据
所用输入
releases_count51
latest_release_tagv1.6.6
releases_from_tags
days_since_latest_release14
mean_days_between_releases35
已排除计分(无数据或不适用):OpenSSF Scorecard:Signed-Releases。 其余权重已重新归一化。

社区与采用

项目是否拥有用户、下载量与关注度,并具备欢迎贡献者参与的配置?

43存在风险 · 占总体的 18%

流行度与采用

37存在风险
评分方式
26.5/60星标 — 44 个星标
7/25复刻 — 8 个复刻
3.9/15关注者 — 6 位关注者
所用输入
forks8
stars44
watchers6
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

社区健康

50中等
评分方式
22.5/22.5README
22.5/22.5许可证 — 可识别的许可证(GPL-3.0)
0/18CONTRIBUTING 指南
0/13.5行为准则
0/7.2议题模板
0/6.3PR 模板
所用输入
has_readme
has_license
has_contributing
has_issue_template
has_code_of_conduct
has_pull_request_template

可持续性与治理

项目能否在其成员之外延续——巴士系数、响应能力、由谁支持,以及软件包的维护状况?

42存在风险 · 占总体的 24%
评分方式
9/54巴士系数 — 1 位贡献者贡献了半数提交
2.4/22.5提交分布 — 头号贡献者编写了 89% 的提交
4.1/13.5贡献者广度 — 3 位贡献者
6/10OpenSSF Scorecard:Contributors — project has 2 contributing companies or organizations -- score normalized to 6
所用输入
bus_factor1
contributors_sampled3
top_contributor_share0.894
评分方式
14.9/46.8议题解决 — 32% 的议题已关闭
38.2/38.3PR 接受 — 已裁定的 PR 中 1/1 已合并
0/15OpenSSF Scorecard:Code-Review — Found 0/30 approved changesets -- score normalized to 0
所用输入
merged_prs1
open_issues30
closed_issues14
issue_closed_ratio0.318
closed_unmerged_prs0
评分方式
10/30所有权背书 — 个人(用户)账户
0/20已验证域名 — 不适用于个人账户
13.9/25所有者影响力 — edgardomortiz 有 84 位关注者
21.3/25既往记录 — 18 个公开仓库,账户约 12 年
所用输入
followers84
owner_typeUser
is_verified
owner_loginedgardomortiz
public_repos18
account_age_days4,660
已排除计分(无数据或不适用):已验证域名。 其余权重已重新归一化。

工程质量

基础的工程与文档实践是否到位?

41存在风险 · 占总体的 20%
评分方式
0/24CI 工作流
0/24存在测试
0/16Linter 配置
0/9.6Pre-commit 钩子
0/6.4.editorconfig
0/20OpenSSF Scorecard:CI-Tests — 无数据
所用输入
has_ci
has_tests
has_editorconfig
has_linter_config
has_precommit_config
已排除计分(无数据或不适用):OpenSSF Scorecard:CI-Tests。 其余权重已重新归一化。

文档

100优秀
评分方式
30/30README
25/25文档目录
15/15文档 / 主页站点 — https://edgardomortiz.github.io/captus.docs/
10/10仓库描述
10/10主题标签 — 16 个主题标签
10/10Wiki
所用输入
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

安全

可见的安全与供应链实践是否稳固,且不存在未解决的高风险司法辖区暴露?

37存在风险 · 占总体的 16%

安全态势

37存在风险
评分方式
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 — 无数据
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 — 无数据
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5许可证 — 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 — 无数据
0/5Pinned-Dependencies — 无数据
0/5SAST — no SAST tool detected
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — 无数据
0/7.5Token-Permissions — 无数据
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
所用输入
sourceopenssf_scorecard
checks_evaluated12
scorecard_versionv5.5.0
checks_inconclusive6
scorecard_aggregate3.7
已排除计分(无数据或不适用):ci_tests, dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions。 其余权重已重新归一化。

AI 就绪度

该仓库在多大程度上具备与 AI 编码代理协同开发与维护的条件?这是一枚独立的实验性徽章——权重为 0.0,因此单独呈现,不影响总体健康评分。

11危急 · 占总体的 0%
评分方式
0/45代理指令 — 没有 CLAUDE.md / AGENTS.md / 编辑器规则
0/15机器可读文档(llms.txt)
11.2/40可读的提交历史 — 100 次人类提交中有 21 次说明了意图(结构化标题或解释性正文)
所用输入
has_llms_txt
legible_history_share0.21
agent_instruction_files
agent_instruction_max_bytes
评分方式
0/18一条命令的引导启动
0/22自动化测试
0/11Lint / 格式化配置
0/11静态类型检查
0/10可复现环境
0/10已体现的代理实践 — 最近 100 次提交中没有代理编写的提交
0/8自动化维护 — 未观察到自动依赖更新
0/10OpenSSF Scorecard:Pinned-Dependencies — 无数据
所用输入
has_nix
has_tests
lockfiles
has_dockerfile
typed_language
bootstrap_files
has_devcontainer
has_linter_config
typecheck_configs
agent_commit_share0
toolchain_manifests
dependency_bot_commit_share0
已排除计分(无数据或不适用):OpenSSF Scorecard:Pinned-Dependencies。 其余权重已重新归一化。
评分方式
0/45可类型检查的代码 — Python,未配置类型检查
39.8/55可控的文件大小 — 采样的 29 个源文件中有 8 个超过 60KB
所用输入
primary_languagePython
largest_source_bytes179,292
source_files_sampled29
oversized_source_files8

关键数据

44GitHub 星标
3贡献者
158最近 12 个月提交数
14距最近推送天数
51发布版本数
1巴士系数(bus factor)
30开放议题
PyPI软件包生态系统数

数据采集警告

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

更多细节

Star 与 Fork 历史 0 ★ / 8 ⇿
0Star
8Fork
50发布

每颗 star 和每个 fork 的添加时间,来自 GitHub 并按天汇总。累计增长位于其构成来源——每日新增——的正上方,二者可相互对照:稳定的自然增长与短暂的突增形态截然不同。当这一差别可被衡量时,它会作为增长真实性予以报告。

02468812021-112024-032026-07
主版本 1次版本 6修订 43

每个点涵盖 5 天。

OpenSSF Scorecard 3.7 / 10
3.7综合

来自开源项目 OpenSSF Scorecard 的独立、工具无关的安全评估。每项检查奖励的是安全实践本身,而非特定供应商的工具。Scorecard 无法判定的检查项标记为 不适用,并从安全评分中剔除(绝不按零分计)。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
不适用CI-Testsno pull request found
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/30 approved changesets -- score normalized to 0
6Contributorsproject has 2 contributing companies or organizations -- score normalized to 6
不适用Dangerous-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
不适用Packagingpackaging workflow not detected
不适用Pinned-Dependenciesno dependencies found
0SASTno SAST tool detected
0Security-Policysecurity policy file not detected
不适用Signed-Releasesno releases found
不适用Token-PermissionsNo tokens found
10Vulnerabilities0 existing vulnerabilities detected
全部依赖 0

来自 GitHub 依赖图的完整解析依赖集合:0 个直接依赖与 0 个间接(传递)软件包。仓库提交锁文件时,传递闭包才是完整的。

注册表软件包版本关系
依赖安全公告 未评估

本报告未能完成公告比对:No resolved dependencies to assess

原始 JSON 报告 机器可读
{
  "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",
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      "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": [
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          "tag": "v1.6.6",
          "kind": "patch",
          "published_at": "2026-07-14T05:35:50Z"
        },
        {
          "tag": "v1.6.5",
          "kind": "patch",
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          "tag": "v1.6.2",
          "kind": "patch",
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        },
        {
          "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"
        },
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          "tag": "v1.5.8",
          "kind": "patch",
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          "tag": "v1.5.7",
          "kind": "patch",
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        },
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          "tag": "v1.5.6",
          "kind": "patch",
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        },
        {
          "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"
        },
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                    "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"
}

评分是信号,而非担保。 评分反映的是 GitHub 上公开可见的实践——不是代码审计,也不是安全保证。

缺失数据将被剔除并重新归一化权重,绝不按零分计。方法论已版本化并公开:指标 v1.13.0、模式 v0.27.0—— 完整方法论 · 指标知识库.

单项结果在整体记录中的位置: 汇总统计.