公开记录
软件健康报告模式 0.27.0 · 指标 1.13.0 · 2026-07-30 20:15 UTC

niekwit / damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

Python · RMIT★ 5 星标⑂ 1 复刻始于 2023年10月在 GitHub 上查看 ↗

niekwit/damid-seq 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(62/100),最低的是AI Readiness(17/100)。 最近一次更新在 31 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

Niek Wit个人账户
11 关注者60 个公开仓库始于 2018年7月University of Cambridge

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?

62中等 · 占总体的 22%

开发活跃度

48存在风险
评分方式
18/36推送新近度 — 最近一次推送于 31 天前
3.5/36提交节奏 — 52 周中有 5 周有提交
16.2/18提交量 — 最近一年 62 次提交
10/10OpenSSF Scorecard:Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
所用输入
commits_last_year62
human_commit_share1
days_since_last_push31
active_weeks_last_year5

发布纪律

84良好
评分方式
27/27有发布版本 — 已发布 5 个发布版本
36/36发布时效 — 最近一次发布版本于 31 天前
12.6/27发布节奏 — 约每 212.4 天发布一次
0/10OpenSSF Scorecard:Signed-Releases — 无数据
所用输入
releases_count5
latest_release_tagv0.7.0
releases_from_tags
days_since_latest_release31
mean_days_between_releases212.4
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?

29危急 · 占总体的 18%
评分方式
9.8/60星标 — 5 个星标
0/25复刻 — 1 个复刻
0/15关注者 — 1 位关注者
所用输入
forks1
stars5
watchers1
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(MIT)
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?

48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
0/22.5提交分布 — 头号贡献者编写了 100% 的提交
1.4/13.5贡献者广度 — 1 位贡献者
3/10OpenSSF Scorecard:Contributors — project has 1 contributing companies or organizations -- score normalized to 3
所用输入
bus_factor1
contributors_sampled1
top_contributor_share1
评分方式
46.8/46.8议题解决 — 100% 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 0/16 approved changesets -- score normalized to 0
所用输入
merged_prs1
open_issues0
closed_issues1
issue_closed_ratio1
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
7.8/25所有者影响力 — niekwit 有 11 位关注者
25/25既往记录 — 60 个公开仓库,账户约 8 年
所用输入
followers11
owner_typeUser
is_verified
owner_loginniekwit
public_repos60
account_age_days2,936
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?

60中等 · 占总体的 20%

工程实践

44存在风险
评分方式
24/24CI 工作流 — 3 个工作流
0/24存在测试
0/16Linter 配置
0/9.6Pre-commit 钩子
0/6.4.editorconfig
20/20OpenSSF Scorecard:CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
所用输入
has_ci
has_tests
has_editorconfig
has_linter_config
has_precommit_config

文档

85优秀
评分方式
30/30README
25/25文档目录
0/15文档 / 主页站点
10/10仓库描述
10/10主题标签 — 3 个主题标签
10/10Wiki
所用输入
topicsbioinformatics-pipeline, damid, snakemake-workflow
has_wiki
homepage
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?

53中等 · 占总体的 16%

安全态势

41存在风险
评分方式
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
2.5/2.5CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/16 approved changesets -- score normalized to 0
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5许可证 — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — 无数据
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — 无数据
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
所用输入
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4.1
已排除计分(无数据或不适用):packaging, signed_releases。 其余权重已重新归一化。
评分方式
35/35直接依赖不含已知公告 — 没有直接依赖携带已知公告
0/25间接依赖不含已知公告 — 在此范围内,传递依赖集合无法与开发和测试依赖区分
0/40没有长期未处理的公告 — 没有公告带有发布日期
所用输入
sourceosv
advisories0
affected_packages0
assessed_packages2
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
已排除计分(无数据或不适用):间接依赖不含已知公告, 没有长期未处理的公告。 其余权重已重新归一化。 已将 2 个已解析依赖与 OSV 比对。 该仓库未发布任何索引可解析的软件包,因此改为评估仓库依赖图。该图将开发与测试版本固定同交付的依赖混在一起,因此仅对声明的运行时依赖计分;传递性发现仅作为背景信息列出,不计入评分。 未对可达性进行分析。

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。

17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)
1.6/40可读的提交历史 — 100 次人类提交中有 3 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_share0.03
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
10/10可复现环境 — Dockerfile
4/10已体现的代理实践 — 最近 100 次提交中有 2 次由代理编写或署名代理
0/8自动化维护 — 未观察到自动依赖更新
0/10OpenSSF Scorecard:Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
所用输入
has_nix
has_tests
lockfiles
has_dockerfile
typed_language
bootstrap_files
has_devcontainer
has_linter_config
typecheck_configs
agent_commit_share0.02
toolchain_manifests
dependency_bot_commit_share0
评分方式
0/45可类型检查的代码 — Python,未配置类型检查
55/55可控的文件大小 — 采样的 15 个源文件中有 0 个超过 60KB
所用输入
primary_languagePython
largest_source_bytes3,693
source_files_sampled15
oversized_source_files0

关键数据

5GitHub 星标
1贡献者
62最近 12 个月提交数
31距最近推送天数
5发布版本数
1巴士系数(bus factor)
0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

更多细节

OpenSSF Scorecard 4.1 / 10
4.1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 · 2026-07-30 20:15 UTC

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

来自 GitHub 依赖图的完整解析依赖集合:0 个直接依赖与 2 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
PyPIsphinx7.3.7间接
PyPIsphinx-rtd-theme2.0.0间接
依赖安全公告 0

该仓库未发布可被索引解析的包,因此评估的是其自身的依赖图——共 2 个包,其中也包含从不交付的开发与测试版本固定:0 个存在已知公告,0 个为直接依赖。

没有已知公告影响已评估的依赖。

公告表示依赖图中记录的版本落入某条公告的受影响范围。可达性未经分析,且依赖图包含开发与测试的版本固定——某项发现可能只涉及工具链而非交付的软件。

原始 JSON 报告 机器可读
{
  "data": {
    "repo": {
      "topics": [
        "bioinformatics-pipeline",
        "damid",
        "snakemake-workflow"
      ],
      "is_fork": false,
      "size_kb": 140060,
      "has_wiki": true,
      "homepage": null,
      "languages": {
        "R": 16919,
        "Perl": 7222,
        "Shell": 644,
        "Python": 112679,
        "Dockerfile": 9761
      },
      "pushed_at": "2026-06-29T09:19:33Z",
      "created_at": "2023-10-21T20:02:14Z",
      "owner_type": "User",
      "updated_at": "2026-06-25T14:51:42Z",
      "description": "DamMapper: Snakemake workflow for DamID-Seq analysis",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "MIT",
      "default_branch": "main",
      "license_spdx_raw": "MIT",
      "primary_language": "Python",
      "significant_languages": [
        "Python",
        "R"
      ]
    },
    "owner": {
      "blog": null,
      "name": "Niek Wit",
      "type": "User",
      "login": "niekwit",
      "company": "University of Cambridge",
      "location": "Cambridge, UK",
      "followers": 11,
      "avatar_url": "https://avatars.githubusercontent.com/u/41302859?v=4",
      "created_at": "2018-07-16T17:17:01Z",
      "is_verified": null,
      "public_repos": 60,
      "account_age_days": 2936
    },
    "license": {
      "state": "standard",
      "spdx_id": "MIT",
      "raw_spdx": "MIT",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [
        {
          "tag": "v0.7.0",
          "kind": "minor",
          "published_at": "2026-06-29T09:19:33Z"
        },
        {
          "tag": "v0.6.0",
          "kind": "minor",
          "published_at": "2025-05-15T14:58:42Z"
        },
        {
          "tag": "v0.5.0",
          "kind": "minor",
          "published_at": "2024-07-05T12:20:41Z"
        },
        {
          "tag": "v0.4.0",
          "kind": "minor",
          "published_at": "2024-04-12T08:28:20Z"
        },
        {
          "tag": "v0.3.0",
          "kind": "minor",
          "published_at": "2024-03-01T21:53:55Z"
        }
      ],
      "recent_commits": [
        {
          "oid": "5e7a30822c6fe17bbd40af01a04734e3077f7499",
          "body": null,
          "is_bot": false,
          "headline": "removed Zenodo badge",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-25T14:52:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "822ee0d13ebd0f98cfc0078f88d02e1fb778b000",
          "body": null,
          "is_bot": false,
          "headline": "point to correct Docker image",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-25T14:52:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "71820c16046b90992eac2d80f959b8dca38edf5d",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind ref sample",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T20:10:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8b435a2c633ec4dcb5d6a42152cacbafe7f13f55",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:55:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "12a5ef70ea699a25becde3de167cdc42ebc53375",
          "body": null,
          "is_bot": false,
          "headline": "improved docs, and added info on damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:54:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86738861086f857f3481ce02ff3ca5d64efd59c9",
          "body": null,
          "is_bot": false,
          "headline": "scaffold skip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:54:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "72482a9aa00d554d4825bdedc9d911a55629872c",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:53:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8dc22a78b0a6d5b5ddab498ab48958270290967f",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:53:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9e2d69d202b573d2b758df9951e8675e6e72a93e",
          "body": null,
          "is_bot": false,
          "headline": "damidBind possible with multiple pairwise comparisons",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8df1e82ccd83f1b8009812e4816cef08bbd82db8",
          "body": null,
          "is_bot": false,
          "headline": "output csv with mapping rates for NGS Tracker",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8ea72af481b80371c07b1e9e57c2fbdcd7d7c14f",
          "body": null,
          "is_bot": false,
          "headline": "damidBind possible with multiple pairwise comparisons",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8d6540ab2c9f221ddd79569a60b2c6e190b45d24",
          "body": null,
          "is_bot": false,
          "headline": "output csv with mapping rates for NGS Tracker",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:13:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a5934fbe3f44a01f0db5eff2b77735caf0d4d219",
          "body": null,
          "is_bot": false,
          "headline": "Integration with NGS Tracker and multiple comaprisons with damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T14:30:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d8a3aaf3dc28a2fbae0dcac8541ea30e843344fa",
          "body": null,
          "is_bot": false,
          "headline": "restrict SE test to index_bam rule, full PE test --> reduce runtime",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T07:11:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f32555f1d8bb3652b2a38475d581ee044bea62fa",
          "body": null,
          "is_bot": false,
          "headline": "deleted one replicate to reduce runtime",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T07:10:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e9c4351047fb71f0bc4c1ec4c49eb06bca450df6",
          "body": "feat: added damidBind analysis",
          "is_bot": false,
          "headline": "Merge pull request #2 from niekwit/damidbind",
          "author_name": "Niek Wit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T05:18:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "39da6a83034155f5f71d0b15d13f9b79fba4f2f2",
          "body": null,
          "is_bot": false,
          "headline": "lowered stringency for test pe",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T21:29:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "64b667aecd176909069376f7a62f15e7f92b92d4",
          "body": null,
          "is_bot": false,
          "headline": "free disk space after se test",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T20:29:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fcfdab95fc3496f8968aeb549f7a4991a2eea28a",
          "body": null,
          "is_bot": false,
          "headline": "use BiocManager::install()",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:40:58Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "62f82c694080c1be7076bb577de7a21d211099f4",
          "body": null,
          "is_bot": false,
          "headline": "fixed bug with conda env cache",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:40:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7ba147a0a34eb1ff7e435e07e3694c2f51149353",
          "body": null,
          "is_bot": false,
          "headline": "activated Perl peak calling for PE test data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:17:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec68cc9fd519f992922e05bcfc3869aa80c91bd9",
          "body": null,
          "is_bot": false,
          "headline": "samples csv included for pe test",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T18:59:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "567695fa3bd2223122a8fae954a6ef479c8fb545",
          "body": null,
          "is_bot": false,
          "headline": "added pe test fastq files",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:48:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "962ad149ed4be8f75c0dbbd089579fb0b0e8a6b6",
          "body": null,
          "is_bot": false,
          "headline": "2 threads for alignment",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:19:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "28ab5c7a72f01987ac4c9053d2add7aaa61c6fd1",
          "body": null,
          "is_bot": false,
          "headline": "no more use of pipe()",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:04:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "64730288282fa4f3218965ee33db84785f4ae95a",
          "body": null,
          "is_bot": false,
          "headline": "disable pathway enrichment analysis for Dm data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:03:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7fe4ef90a89eb2f4f4aa7aea72eccab1d68f2fe6",
          "body": null,
          "is_bot": false,
          "headline": "fixed broken counter",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:53:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f9f7791a84a5dc06d84711c4c007d0d03ef429e1",
          "body": null,
          "is_bot": false,
          "headline": "changed resource cpu counts to 1",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:45:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0bb461d65aebd15edc13bc9250c1606e1202dc1b",
          "body": null,
          "is_bot": false,
          "headline": "enabled PE testing",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:44:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c7bfa05ee74f407ee5923838a6606af086befcdd",
          "body": "The old script installed damidBind into the damid conda environment.\ndamidBind now has its own environment (damidbind.yaml) with a dedicated\npost-deploy script, so this file is no longer needed.\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Remove damid.post-deploy.sh (damidBind moved to damidbind env)",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:27:56Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "5ed6d571605303590cea4027df80e35b1319cd98",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:19:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1ab38ac85373eb876f7f073c56bf6ac32dc2a37c",
          "body": null,
          "is_bot": false,
          "headline": "import resources as alias",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:16:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "50cad760403440a9180a0226ce48842cbe3f470f",
          "body": "Resolved conflicts in favour of damidbind branch:\n- Dockerfile/README: new damidbind conda env, updated hashes, pinned v1.1.1\n- Snakefile: keep VERSION = \"v0.7.0\"\n- damid.yaml: keep wget, drop r-biocmanager (moved to damidbind env)\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Merge origin/main into damidbind, keeping damidbind changes",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:10:19Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "6a8fc6859c0cdff81aeea0f380541718c7a2f34c",
          "body": null,
          "is_bot": false,
          "headline": "damidBind working now with test data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T12:59:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a73acac7b017a3e040aef644c0db59b09ecbf629",
          "body": null,
          "is_bot": false,
          "headline": "pin version to v1.1.1",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T12:59:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c02cc82a1bd5caa58b45865df60060fad4b57adb",
          "body": null,
          "is_bot": false,
          "headline": "added wget",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T08:10:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "975ba68c92867cca4e8dedee97e976ba80ec934b",
          "body": null,
          "is_bot": false,
          "headline": "do not update other packages when installing BioVenn of damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T08:10:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0db9a39c16c3761c1c2efac5cf035c1d8c4a259b",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:26:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "277fc92c748fecd3424541cee31619bc29b8b20f",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind rule",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:24:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "276d151289532397484aa0c44c7e1a82e4f286df",
          "body": null,
          "is_bot": false,
          "headline": "Initial commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:24:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6c9d8bc21312ae37a5d0e4514ee39abe8dafbe73",
          "body": null,
          "is_bot": false,
          "headline": "installation of damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:23:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7e5614b72f5daa5bf26f6595b181d1ba1afe6332",
          "body": null,
          "is_bot": false,
          "headline": "v0.7.0, keep just one Dockerfile",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:22:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "95310a6b67a380bfceb0552dae1b4b9ec189c440",
          "body": "… only",
          "is_bot": false,
          "headline": "added post-deploy script to install damidBind when running with Conda…",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T10:10:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "101bb8b99f82f6f440bf2ddb9ff687b2123430d6",
          "body": null,
          "is_bot": false,
          "headline": "fixed error with non-existing command",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:57:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "963e769767fa551aed5e27415ffb245d621defd1",
          "body": null,
          "is_bot": false,
          "headline": "changed df concatenation to avoid FutureWarning",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:56:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "85f4f0e5cff0658b769fcf2fe45fd43019c3e095",
          "body": null,
          "is_bot": false,
          "headline": "deleted",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:28:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86ae97895fea03c5cb16fcdd02585b1985f368f0",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:27:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9b39f4c762c7a83907c7f2c3fdadb8f3d7e9a18f",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:23:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "511e2cb8af4890fdf93c58e0ac43dddf704c6c44",
          "body": null,
          "is_bot": false,
          "headline": "one Dockerfile",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:22:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ad29d903b04d23c1e774ac9b473c6632079de7a1",
          "body": null,
          "is_bot": false,
          "headline": "added biocmanager",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:00:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f58f6caf56b5f32c3c7d4e265155a814333247df",
          "body": null,
          "is_bot": false,
          "headline": "r-base=4.3.2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:47:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cab659bd0d64c9ce467b976e3d1b5ff575d45131",
          "body": null,
          "is_bot": false,
          "headline": "changed dir name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:40:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e285842bdd58cdf6e39a9a25f630b90f0af333b6",
          "body": null,
          "is_bot": false,
          "headline": "added missing validations",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:40:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cdac1091c4107439e730f413bd836ea08d125e2b",
          "body": null,
          "is_bot": false,
          "headline": "changed replacement string",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:39:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "597d2b52216017344925d7229bf316e2910fd869",
          "body": null,
          "is_bot": false,
          "headline": "moved code to general_functions.smk",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:38:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0fd79ded8d513da51481d058ced2d8613f04e14",
          "body": null,
          "is_bot": false,
          "headline": "bumped to v0.7.0",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:36:19Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c86e1bf512f3c64e5d2b1a9927199736c35db9b9",
          "body": "Added citation information for DamMapper.",
          "is_bot": false,
          "headline": "Add citation section to README",
          "author_name": "Niek Wit",
          "author_login": "niekwit",
          "committed_at": "2025-10-15T20:00:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "71dad9a10e08174f9bda575aa4953127d49bd2e4",
          "body": null,
          "is_bot": false,
          "headline": "changed git version to 2.49",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:55:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d5d2921628c21eeca0aa704b0572abb8f3e3ecc3",
          "body": null,
          "is_bot": false,
          "headline": "changed r version",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:18:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "021f73b3166835fb09f8e65676d18f9a4c96f9fa",
          "body": null,
          "is_bot": false,
          "headline": "added git",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:00:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "88946ca4ba759b75f1ce01dd9ba8d559b0378e89",
          "body": null,
          "is_bot": false,
          "headline": "point to specific commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-28T14:37:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f8cf4168ceae10e609ff90906ea7dada00814278",
          "body": null,
          "is_bot": false,
          "headline": "added splash screen",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-28T13:21:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1e9cd843fd175f6b6ef9854240b02f6b3daaad1e",
          "body": null,
          "is_bot": false,
          "headline": "replaced damid-seq with DamMapper",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-06-04T09:07:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0d7cce4762506e9a6e6fc5156077c16853c981d5",
          "body": null,
          "is_bot": false,
          "headline": "replaced damid-seq with DamMapper",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-06-04T09:02:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c072bc27194e45b584b6f5d5a506b36ad6365f4e",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-05-14T07:17:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "252ae1d9b0102aa9c1b3da115c4d80ec8ca8f2d0",
          "body": null,
          "is_bot": false,
          "headline": "changed name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-15T14:23:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "15cfeca08063e3e47fee509fbcf3f09466d9d9e2",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:49:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "50cfe153f52ccf64fb2cf5ef0d3fc3776f38ee4d",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 4",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:46:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5ad401e4ba84788f8c5fcae6241652d1b3f93642",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:37:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c9a2253200955995afa44efb963938499108530c",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:21:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d5de8ded48fede3dfb89b2b858e305b01264f93c",
          "body": null,
          "is_bot": false,
          "headline": "updated name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:26:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "154427fe2668ad5f8284acab59472f49f05f83b8",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:25:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5cb2f9452875cab849deb7f7f333dd38f9161ac8",
          "body": null,
          "is_bot": false,
          "headline": "Air formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:24:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86e342944af1cb9b8a91d48ab7b87b91fbfe227d",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:18:59Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ebe4205e0ae3399678ef9373de4e892223c1cebe",
          "body": null,
          "is_bot": false,
          "headline": "sort gatc gff file",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:18:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "076c707704ece74c789ec59d5216997de6fdda33",
          "body": null,
          "is_bot": false,
          "headline": "changed path",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:12:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d499bd2b774c417cb5ea41ee5c83063e0cd87430",
          "body": null,
          "is_bot": false,
          "headline": "added warning after completion",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:10:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "edeba6a6ca106fe47df429fb948f9c73c401c818",
          "body": null,
          "is_bot": false,
          "headline": "added mm38",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a1b8c47d7cadb39462f5cc1e38f120c632161eaa",
          "body": null,
          "is_bot": false,
          "headline": "added mm38",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "18907a06f937acc19a307d730e107e96100c2427",
          "body": null,
          "is_bot": false,
          "headline": "check for plasmid function",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "78e45e5dd239a5e8aa80f040185f5ade5a0fe72c",
          "body": null,
          "is_bot": false,
          "headline": "simplified frip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a129736b69864c42f342dc4c4d54f60603cbbc36",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9bff7ddda224d4c15ae84c0df194c7b8ce9f591b",
          "body": null,
          "is_bot": false,
          "headline": "simplified frip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c81f1dd21674ffcb3bacd333b6160f8b1e85bacb",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:20:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "019132e43da0766a830e075c275f6932d0b9234f",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:20:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f2da3fc8a71b596f21c1f670b282375a496a3876",
          "body": null,
          "is_bot": false,
          "headline": "removed redundant code",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:19:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "17da854cd478da5014120d6702bfbd0da349a1e8",
          "body": null,
          "is_bot": false,
          "headline": "fixed issues with input/output and added samtools flag",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:19:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "414c13500fd81ba1cefe1bc1a1b9bc40eb01b7e2",
          "body": null,
          "is_bot": false,
          "headline": "Initial commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-03T09:54:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9fe66b06549280d2507c1c41e2f987288bf59fe1",
          "body": null,
          "is_bot": false,
          "headline": "simplified",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T14:27:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7c56263b0def4bf7f22fb01ff53ccd1bca79ce82",
          "body": null,
          "is_bot": false,
          "headline": "added pybedtools",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T11:17:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "813a5dc484a5daf1091a88d0921bbcd88a839afc",
          "body": null,
          "is_bot": false,
          "headline": "added pybedtools",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T10:55:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9d478360ff4f2977b05651ef7de896c003255818",
          "body": null,
          "is_bot": false,
          "headline": "remove duplicate peaks",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-01T13:21:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ed0a8cb99f22defa6527eb799f0d54670dca1d97",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:52:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "deb586c3d549d21b02a32a29f45e0e2643b9cf60",
          "body": null,
          "is_bot": false,
          "headline": "wrapper v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:16:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6a281190424bcd26ea35e1c3adda3e8694546e03",
          "body": null,
          "is_bot": false,
          "headline": "Changed versions of wrappers and Snakemake",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:15:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9061bfb94957721b0a8c7c1d617bcf75327e680f",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T09:16:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "237dc19ac6df1d6388e0a2d3713b40c8bcf228f8",
          "body": null,
          "is_bot": false,
          "headline": "deleted",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T08:48:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c94e0364796bc6fff37973edbfed5a48b9ce347f",
          "body": null,
          "is_bot": false,
          "headline": "increased CPU count for bowtie2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T15:32:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "da49a6b8e45d554e56fc22d2bf9672e1671b6f6b",
          "body": null,
          "is_bot": false,
          "headline": "lowered CPU count",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T15:12:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "457ca120a0ccfc632547ce915af1364a8b54db95",
          "body": null,
          "is_bot": false,
          "headline": "working again",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T14:58:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        }
      ],
      "releases_count": 5,
      "commits_last_year": 62,
      "latest_release_at": "2026-06-29T09:19:33Z",
      "latest_release_tag": "v0.7.0",
      "releases_from_tags": false,
      "days_since_last_push": 31,
      "active_weeks_last_year": 5,
      "days_since_latest_release": 31,
      "mean_days_between_releases": 212.4
    },
    "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": 1,
      "stars": 5,
      "watchers": 1,
      "fork_history": {
        "days": [
          {
            "date": "2026-04-04",
            "count": 1
          }
        ],
        "complete": true,
        "collected": 1,
        "total_forks": 1
      },
      "star_history": null,
      "open_issues_and_prs": 0
    },
    "ai_readiness": {
      "has_nix": false,
      "example_dirs": [],
      "has_llms_txt": false,
      "has_dockerfile": true,
      "has_mcp_signal": false,
      "bootstrap_files": [],
      "api_schema_files": [],
      "has_devcontainer": false,
      "typecheck_configs": [],
      "toolchain_manifests": [],
      "largest_source_bytes": 3693,
      "source_files_sampled": 15,
      "oversized_source_files": 0,
      "agent_instruction_files": [],
      "agent_instruction_max_bytes": null
    },
    "dependencies": {
      "manifests": [
        "docs/requirements.txt"
      ],
      "advisories": {
        "error": null,
        "scope": "repository_graph",
        "source": "osv",
        "findings": [],
        "collected": true,
        "malicious": [],
        "truncated": false,
        "by_severity": {},
        "advisory_count": 0,
        "affected_count": 0,
        "assessed_count": 2,
        "malicious_count": 0,
        "assessed_package": null,
        "unassessed_count": 0,
        "direct_affected_count": 0
      },
      "ecosystems": [
        "pypi"
      ],
      "dependencies": [],
      "all_dependencies": {
        "error": null,
        "source": "github-sbom",
        "packages": [
          {
            "name": "sphinx",
            "direct": false,
            "version": "7.3.7",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-rtd-theme",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          }
        ],
        "collected": true,
        "truncated": false,
        "total_count": 2,
        "direct_count": 0,
        "indirect_count": 2
      }
    },
    "maintainership": {
      "issues": {
        "open_prs": 0,
        "merged_prs": 1,
        "open_issues": 0,
        "closed_ratio": 1,
        "closed_issues": 1,
        "closed_unmerged_prs": 0
      },
      "bus_factor": 1,
      "bot_contributors": 0,
      "top_contributors": [
        {
          "type": "User",
          "login": "niekwit",
          "commits": 514,
          "avatar_url": "https://avatars.githubusercontent.com/u/41302859?v=4"
        }
      ],
      "contributors_sampled": 1,
      "top_contributor_share": 1
    },
    "quality_signals": {
      "has_ci": true,
      "has_tests": false,
      "ci_workflows": [
        "conventional-prs.yml",
        "main.yml",
        "release-please.yml"
      ],
      "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": 10,
            "reason": "no binaries found in the repo",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
          },
          {
            "name": "Branch-Protection",
            "score": 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": 10,
            "reason": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
            "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 0/16 approved changesets -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 3,
            "reason": "project has 1 contributing companies or organizations -- score normalized to 3",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": 10,
            "reason": "no dangerous workflow patterns detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
          {
            "name": "Dependency-Update-Tool",
            "score": 0,
            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
          },
          {
            "name": "Fuzzing",
            "score": 0,
            "reason": "project is not fuzzed",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
          },
          {
            "name": "License",
            "score": 10,
            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
          },
          {
            "name": "Maintained",
            "score": 10,
            "reason": "30 commit(s) and 0 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": 0,
            "reason": "dependency not pinned by hash detected -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "SAST tool is not run on all commits -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
          },
          {
            "name": "Security-Policy",
            "score": 0,
            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
          },
          {
            "name": "Signed-Releases",
            "score": null,
            "reason": "no releases found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
          },
          {
            "name": "Token-Permissions",
            "score": 0,
            "reason": "detected GitHub workflow tokens with excessive permissions",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
          {
            "name": "Vulnerabilities",
            "score": 10,
            "reason": "0 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
          }
        ],
        "commit": "5e7a30822c6fe17bbd40af01a04734e3077f7499",
        "ran_at": "2026-07-30T20:15:44Z",
        "aggregate_score": 4.1,
        "scorecard_version": "v5.5.0"
      },
      "has_codeql_workflow": false,
      "has_security_policy": false,
      "has_dependabot_config": false
    },
    "contribution_flow": {
      "collected": true,
      "ci_last_run_at": "2026-06-29T09:04:38Z",
      "oldest_open_prs": [],
      "last_merged_pr_at": "2026-06-24T05:18:08Z",
      "ci_last_conclusion": "SUCCESS",
      "oldest_open_issues": []
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/niekwit/damid-seq",
    "host": "github.com",
    "name": "damid-seq",
    "owner": "niekwit"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "moderate",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 51,
      "inputs": {
        "security": 53,
        "vitality": 62,
        "community": 29,
        "governance": 48,
        "engineering": 60
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "moderate",
        "name": "Vitality",
        "value": 62,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "at_risk",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 48,
            "inputs": {
              "commits_last_year": 62,
              "human_commit_share": 1,
              "days_since_last_push": 31,
              "active_weeks_last_year": 5
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 31 days ago",
                "points": 18,
                "status": "partial",
                "details": [
                  {
                    "code": "push_recency",
                    "params": {
                      "days": 31
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "5/52 weeks with commits",
                "points": 3.5,
                "status": "partial",
                "details": [
                  {
                    "code": "commit_cadence_weeks",
                    "params": {
                      "weeks": 5
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "62 commits in the last year",
                "points": 16.2,
                "status": "partial",
                "details": [
                  {
                    "code": "commits_last_year",
                    "params": {
                      "count": 62
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "release_discipline",
            "band": "good",
            "name": "Release discipline",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 84,
            "inputs": {
              "releases_count": 5,
              "latest_release_tag": "v0.7.0",
              "releases_from_tags": false,
              "days_since_latest_release": 31,
              "mean_days_between_releases": 212.4
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "5 releases published",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "releases_published",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "latest release 31 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "release_recency",
                    "params": {
                      "days": 31
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "a release every ~212.4 days",
                "points": 12.6,
                "status": "partial",
                "details": [
                  {
                    "code": "release_cadence",
                    "params": {
                      "gap": 212.4
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "openssf_scorecard_signed_releases",
                "name": "OpenSSF Scorecard: Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              }
            ]
          },
          {
            "key": "abandonment",
            "band": "excellent",
            "name": "Abandonment",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "cap": null,
              "state": "maintained",
              "guards": [],
              "signals": [],
              "red_flag": false,
              "multiplier_pct": 100,
              "declared_reason": null,
              "unverified_reason": null,
              "unanswered_open_prs": null,
              "unanswered_open_issues": null,
              "days_since_last_merged_pr": null,
              "days_since_last_human_commit": 35,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 35 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 35
                    }
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "critical",
        "name": "Community & Adoption",
        "value": 29,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "critical",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 10,
            "inputs": {
              "forks": 1,
              "stars": 5,
              "watchers": 1,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "5 stars",
                "points": 9.8,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "1 forks",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "1 watchers",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "moderate",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": false,
              "has_issue_template": false,
              "has_code_of_conduct": false,
              "has_pull_request_template": false
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 22.5,
                "status": "met",
                "details": [],
                "max_points": 22.5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "recognized license (MIT)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "MIT"
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 18
              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 13.5
              },
              {
                "key": "issue_template",
                "name": "Issue template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
              },
              {
                "key": "pr_template",
                "name": "PR template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.3
              }
            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
      },
      {
        "key": "governance",
        "band": "at_risk",
        "name": "Sustainability & Governance",
        "value": 48,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "critical",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 13,
            "inputs": {
              "bus_factor": 1,
              "contributors_sampled": 1,
              "top_contributor_share": 1
            },
            "components": [
              {
                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "1 contributor(s) cover half of all commits",
                "points": 9,
                "status": "partial",
                "details": [
                  {
                    "code": "bus_factor",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 54
              },
              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 100% of commits",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
                "points": 1.4,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 3,
                "status": "partial",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "excellent",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "merged_prs": 1,
              "open_issues": 0,
              "closed_issues": 1,
              "issue_closed_ratio": 1,
              "closed_unmerged_prs": 0
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "100% of issues closed",
                "points": 46.8,
                "status": "met",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "1/1 decided PRs merged",
                "points": 38.2,
                "status": "met",
                "details": [
                  {
                    "code": "decided_prs_merged",
                    "params": {
                      "merged": 1,
                      "decided": 1
                    }
                  }
                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 0/16 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "moderate",
            "name": "Ownership & stewardship",
            "note": "Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "verified_domain"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 54,
            "inputs": {
              "followers": 11,
              "owner_type": "User",
              "is_verified": null,
              "owner_login": "niekwit",
              "public_repos": 60,
              "account_age_days": 2936
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "personal (user) account",
                "points": 10,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_personal",
                    "params": {}
                  }
                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": "not applicable to user accounts",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "not_applicable_to_user_accounts",
                    "params": {}
                  }
                ],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "11 followers of niekwit",
                "points": 7.8,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 11,
                      "login": "niekwit"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "60 public repos, account ~8 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 60
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 8
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "moderate",
        "name": "Engineering Quality",
        "value": 60,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "at_risk",
            "name": "Engineering practices",
            "note": null,
            "notes": [],
            "value": 44,
            "inputs": {
              "has_ci": true,
              "has_tests": false,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "3 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 9.6
              },
              {
                "key": "editorconfig",
                "name": ".editorconfig",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 20,
                "status": "met",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "topics": [
                "bioinformatics-pipeline",
                "damid",
                "snakemake-workflow"
              ],
              "has_wiki": true,
              "homepage": null,
              "has_readme": true,
              "has_docs_dir": true,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 25,
                "status": "met",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "3 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "moderate",
        "name": "Security",
        "value": 53,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "packaging",
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 41,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 16,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 2,
              "scorecard_aggregate": 4.1
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "branch_protection",
                "name": "Branch-Protection",
                "detail": "branch protection not enabled on development/release branches",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 0/16 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 0.8,
                "status": "partial",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no dangerous workflow patterns detected",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "excellent",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories",
                    "no_advisories_left_outstanding"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 2
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "source": "osv",
              "advisories": 0,
              "affected_packages": 0,
              "assessed_packages": 2,
              "unassessed_packages": 0,
              "affected_by_severity": "none",
              "direct_affected_packages": 0
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "no direct dependency carries a known advisory",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "no_direct_advisories",
                    "params": {}
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory carries a publication date",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_no_publication_date",
                    "params": {}
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 2,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
            },
            "components": [
              {
                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 2
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "critical",
        "name": "AI Readiness",
        "value": 17,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 2,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.03,
              "agent_instruction_files": [],
              "agent_instruction_max_bytes": null
            },
            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "no CLAUDE.md / AGENTS.md / editor rules",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_instructions",
                    "params": {}
                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "3 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 1.6,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 3,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "critical",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 14,
            "inputs": {
              "has_nix": false,
              "has_tests": false,
              "lockfiles": [],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [],
              "agent_commit_share": 0.02,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "Dockerfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "2 of the last 100 commits agent-authored or agent-credited",
                "points": 4,
                "status": "partial",
                "details": [
                  {
                    "code": "agent_authored_commits",
                    "params": {
                      "count": 2,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
              "primary_language": "Python",
              "largest_source_bytes": 3693,
              "source_files_sampled": 15,
              "oversized_source_files": 0
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Python without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "Python"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "0/15 source files over 60KB",
                "points": 55,
                "status": "met",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 15,
                      "oversized": 0
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-30T20:15:58.825981Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/n/niekwit/damid-seq.svg",
  "full_name": "niekwit/damid-seq",
  "license_state": "standard",
  "license_spdx": "MIT"
}

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.