公开记录良好
软件健康报告模式 0.23.0 · 指标 1.13.0 · 2026-07-21 20:30 UTC
pysam-developers / pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
pysam-developers/pysam 的健康指数为 100 分中的 73 分，处于「良好」区间。 其得分最高的类别是Vitality（85/100），最低的是AI Readiness（51/100）。 最近一次更新在 2 天前。 近期的大部分工作由 1 位贡献者完成。
73
总分 / 100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。
73
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）
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
软件包生态系统
| 注册表 | 软件包 | 版本 | 月下载量 | 版本数 | 最近发布 |
|---|---|---|---|---|---|
| PyPI | pysam | 0.24.0 | 1,150,697 | 48 | 85 天前 |
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？
85
开发活跃度
86优秀
评分方式
| 36/36 | 推送新近度 — 最近一次推送于 2 天前 |
| 22.8/36 | 提交节奏 — 52 周中有 33 周有提交 |
| 17.3/18 | 提交量 — 最近一年 84 次提交 |
| 10/10 | OpenSSF Scorecard：Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
所用输入
| commits_last_year | 84 |
| human_commit_share | 1 |
| days_since_last_push | 2 |
| active_weeks_last_year | 33 |
发布纪律
84良好
评分方式
| 27/27 | 有发布版本 — 已发布 41 个发布版本 |
| 36/36 | 发布时效 — 最近一次发布版本于 85 天前 |
| 12.6/27 | 发布节奏 — 约每 159.1 天发布一次 |
| 0/10 | OpenSSF Scorecard：Signed-Releases — 无数据 |
所用输入
| releases_count | 41 |
| latest_release_tag | v0.24.0 |
| releases_from_tags | 否 |
| days_since_latest_release | 85 |
| mean_days_between_releases | 159.1 |
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？
74
流行度与采用
78良好
评分方式
| 47.9/60 | 星标 — 900 个星标 |
| 20.6/25 | 复刻 — 297 个复刻 |
| 9/15 | 关注者 — 42 位关注者 |
所用输入
| forks | 297 |
| stars | 900 |
| watchers | 42 |
| growth_state | organic |
| growth_factor_pct | 100 |
社区健康
50中等
评分方式
| 22.5/22.5 | README |
| 22.5/22.5 | 许可证 — 可识别的许可证（MIT） |
| 0/18 | CONTRIBUTING 指南 |
| 0/13.5 | 行为准则 |
| 0/7.2 | 议题模板 |
| 0/6.3 | PR 模板 |
所用输入
| has_readme | 是 |
| has_license | 是 |
| has_contributing | 否 |
| has_issue_template | 否 |
| has_code_of_conduct | 否 |
| has_pull_request_template | 否 |
生态采用（下载量）
100优秀
评分方式
| 80/80 | 月度下载量 — pypi 合计每月 1,150,697 次下载 |
| 0/20 | 注册表被依赖数 — 该生态系统不报告此项 |
所用输入
| packages | pysam |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 1,150,697 |
已排除计分（无数据或不适用）：注册表被依赖数。 其余权重已重新归一化。
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？
63
维护者韧性（巴士系数）
42存在风险
评分方式
| 9/54 | 巴士系数 — 1 位贡献者贡献了半数提交 |
| 9.2/22.5 | 提交分布 — 头号贡献者编写了 59% 的提交 |
| 13.5/13.5 | 贡献者广度 — 100 位贡献者 |
| 10/10 | OpenSSF Scorecard：Contributors — project has 27 contributing companies or organizations |
所用输入
| bus_factor | 1 |
| contributors_sampled | 100 |
| top_contributor_share | 0.589 |
议题与 PR 响应能力
67中等
评分方式
| 35.2/46.8 | 议题解决 — 75% 的议题已关闭 |
| 32/38.3 | PR 接受 — 已裁定的 PR 中 344/411 已合并 |
| 0/15 | OpenSSF Scorecard：Code-Review — Found 1/27 approved changesets -- score normalized to 0 |
所用输入
| merged_prs | 344 |
| open_issues | 242 |
| closed_issues | 734 |
| issue_closed_ratio | 0.752 |
| closed_unmerged_prs | 67 |
所有权与托管责任
54中等
评分方式
| 30/30 | 所有权背书 — 组织持有 |
| 0/20 | 已验证域名 |
| 7.5/25 | 所有者影响力 — pysam-developers 有 10 位关注者 |
| 16.4/25 | 既往记录 — 3 个公开仓库，账户约 12 年 |
所用输入
| followers | 10 |
| owner_type | Organization |
| is_verified | — |
| owner_login | pysam-developers |
| public_repos | 3 |
| account_age_days | 4,548 |
软件包维护
100优秀
评分方式
| 25/25 | 已发布且可解析 — pypi 上有 1 个软件包 |
| 35/35 | 发布时效 — 最近一次发布于 85 天前 |
| 20/20 | 版本历史 — 48 个已发布版本 |
| 20/20 | 未被弃用 — 活跃，未被弃用或撤回 |
所用输入
| packages | pysam |
| ecosystems | pypi |
| any_deprecated | 否 |
| min_days_since_publish | 85 |
工程质量
基础的工程与文档实践是否到位？
81
工程实践
68中等
评分方式
| 24/24 | CI 工作流 — 2 个工作流 |
| 24/24 | 存在测试 |
| 0/16 | Linter 配置 |
| 0/9.6 | Pre-commit 钩子 |
| 0/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard：CI-Tests — 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
所用输入
| has_ci | 是 |
| has_tests | 是 |
| has_editorconfig | 否 |
| has_linter_config | 否 |
| has_precommit_config | 否 |
文档
100优秀
评分方式
| 30/30 | README |
| 25/25 | 文档目录 |
| 15/15 | 文档 / 主页站点 — https://pysam.readthedocs.io/en/latest/ |
| 10/10 | 仓库描述 |
| 10/10 | 主题标签 — 4 个主题标签 |
| 10/10 | Wiki |
所用输入
| topics | bioinformatics, ngs, python, htslib |
| has_wiki | 是 |
| homepage | https://pysam.readthedocs.io/en/latest/ |
| has_readme | 是 |
| has_docs_dir | 是 |
| has_description | 是 |
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？
59
安全态势
49存在风险
评分方式
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 4.5/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 1/27 approved changesets -- score normalized to 0 |
| 2.5/2.5 | Contributors — project has 27 contributing companies or organizations |
| 0/10 | Dangerous-Workflow — 无数据 |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | 许可证 — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
| 0/5 | Packaging — 无数据 |
| 0/5 | Pinned-Dependencies — 无数据 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — 无数据 |
| 0/7.5 | Token-Permissions — 无数据 |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
所用输入
| source | openssf_scorecard |
| checks_evaluated | 13 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 5 |
| scorecard_aggregate | 4.9 |
已排除计分（无数据或不适用）：dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions。 其余权重已重新归一化。
依赖安全公告
100优秀
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
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 2 |
| unassessed_packages | 2 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
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。 有 2 项无法评估——没有已解析的版本、生态系统不受支持，或超出所报告的软件包清单。 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。
51
AI 代理上下文与指引
32存在风险
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） |
| 31.5/40 | 可读的提交历史 — 100 次人类提交中有 59 次说明了意图（结构化标题或解释性正文） |
所用输入
| has_llms_txt | 否 |
| legible_history_share | 0.59 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
评分方式
| 18/18 | 一条命令的引导启动 — doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile |
| 22/22 | 自动化测试 |
| 0/11 | Lint / 格式化配置 |
| 11/11 | 静态类型检查 — pysam/py.typed |
| 0/10 | 可复现环境 |
| 0/10 | 已体现的代理实践 — 最近 100 次提交中没有代理编写的提交 |
| 0/8 | 自动化维护 — 未观察到自动依赖更新 |
| 0/10 | OpenSSF Scorecard：Pinned-Dependencies — 无数据 |
所用输入
| has_nix | 否 |
| has_tests | 是 |
| lockfiles | — |
| has_dockerfile | 否 |
| typed_language | 否 |
| bootstrap_files | doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile |
| has_devcontainer | 否 |
| has_linter_config | 否 |
| typecheck_configs | pysam/py.typed |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
已排除计分（无数据或不适用）：OpenSSF Scorecard：Pinned-Dependencies。 其余权重已重新归一化。
面向模型的代码可读性
75良好
评分方式
| 27/45 | 可类型检查的代码 — Cython，已配置类型检查（pysam/py.typed） |
| 48.3/55 | 可控的文件大小 — 采样的 458 个源文件中有 56 个超过 60KB |
所用输入
| primary_language | Cython |
| largest_source_bytes | 230,215 |
| source_files_sampled | 458 |
| oversized_source_files | 56 |
关键数据
900GitHub 星标
100贡献者
84最近 12 个月提交数
2距最近推送天数
41发布版本数
1巴士系数（bus factor）
242开放议题
PyPI软件包生态系统数
数据采集警告
- Could not fetch pypi package 'pysam.libchtslib' from its registry
更多细节
Star 与 Fork 历史 900 ★ / 297 ⇿
900Star
297Fork
41发布
每颗 star 和每个 fork 的添加时间，来自 GitHub 并按天汇总。累计增长位于其构成来源——每日新增——的正上方，二者可相互对照：稳定的自然增长与短暂的突增形态截然不同。当这一差别可被衡量时，它会作为增长真实性予以报告。
主版本 0次版本 15修订 17
每个点涵盖 12 天。
OpenSSF Scorecard 4.9 / 10
4.9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）。
| 10 | Binary-Artifacts | no binaries found in the repo |
| 6 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 1/27 approved changesets -- score normalized to 0 |
| 10 | Contributors | project has 27 contributing companies or organizations |
| 不适用 | Dangerous-Workflow | no workflows found |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
| 不适用 | Packaging | packaging workflow not detected |
| 不适用 | Pinned-Dependencies | no dependencies found |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| 不适用 | Signed-Releases | no releases found |
| 不适用 | Token-Permissions | No tokens found |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
全部依赖 4
来自 GitHub 依赖图的完整解析依赖集合：0 个直接依赖与 4 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 |
|---|---|---|---|
| PyPI | cython | — | 间接 |
| PyPI | setuptools | — | 间接 |
| PyPI | sphinx | 8.2.3 | 间接 |
| PyPI | sphinx-rtd-theme | 3.0.2 | 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。 有 2 个无法评估——没有已解析的版本、生态系统不受支持，或不在所列包清单之内。
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",
"ngs",
"python",
"htslib"
],
"is_fork": false,
"size_kb": 20814,
"has_wiki": true,
"homepage": "https://pysam.readthedocs.io/en/latest/",
"languages": {
"C": 95096,
"Shell": 2341,
"Cython": 665345,
"Python": 436030,
"Makefile": 3880
},
"pushed_at": "2026-07-19T19:36:52Z",
"created_at": "2014-02-05T20:38:10Z",
"owner_type": "Organization",
"updated_at": "2026-07-21T16:18:41Z",
"description": "Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.",
"is_archived": false,
"is_disabled": false,
"license_spdx": "MIT",
"default_branch": "master",
"license_spdx_raw": "MIT",
"primary_language": "Cython",
"significant_languages": [
"Cython",
"Python"
]
},
"owner": {
"blog": null,
"name": null,
"type": "Organization",
"login": "pysam-developers",
"company": null,
"location": null,
"followers": 10,
"avatar_url": "https://avatars.githubusercontent.com/u/6598771?v=4",
"created_at": "2014-02-05T20:36:20Z",
"is_verified": null,
"public_repos": 3,
"account_age_days": 4548
},
"license": {
"state": "standard",
"spdx_id": "MIT",
"raw_spdx": "MIT",
"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases": [
{
"tag": "v0.24.0",
"kind": "minor",
"published_at": "2026-04-27T12:28:44Z"
},
{
"tag": "v0.23.3",
"kind": "patch",
"published_at": "2025-06-10T11:24:09Z"
},
{
"tag": "v0.23.2",
"kind": "patch",
"published_at": "2025-06-06T09:16:15Z"
},
{
"tag": "v0.23.1",
"kind": "patch",
"published_at": "2025-05-28T13:33:03Z"
},
{
"tag": "v0.23.0",
"kind": "minor",
"published_at": "2025-02-05T10:29:53Z"
},
{
"tag": "v0.22.1",
"kind": "patch",
"published_at": "2024-04-24T00:36:32Z"
},
{
"tag": "v0.22.0",
"kind": "minor",
"published_at": "2023-10-05T09:36:15Z"
},
{
"tag": "v0.21.0",
"kind": "minor",
"published_at": "2023-04-01T21:16:44Z"
},
{
"tag": "v0.20.0",
"kind": "minor",
"published_at": "2022-10-28T13:46:15Z"
},
{
"tag": "v0.19.1",
"kind": "patch",
"published_at": "2022-05-26T19:16:09Z"
},
{
"tag": "v0.19.0",
"kind": "minor",
"published_at": "2022-03-29T19:12:07Z"
},
{
"tag": "v0.18.0",
"kind": "minor",
"published_at": "2021-11-16T12:44:48Z"
},
{
"tag": "v0.17.0",
"kind": "minor",
"published_at": "2021-09-30T08:39:44Z"
},
{
"tag": "v0.16.0.1",
"kind": "other",
"published_at": "2020-06-16T23:04:57Z"
},
{
"tag": "v0.16.0",
"kind": "minor",
"published_at": "2020-06-07T20:42:50Z"
},
{
"tag": "v0.15.4",
"kind": "patch",
"published_at": "2020-01-19T20:54:33Z"
},
{
"tag": "v0.15.3",
"kind": "patch",
"published_at": "2019-07-28T20:06:08Z"
},
{
"tag": "v0.15.2",
"kind": "patch",
"published_at": "2019-01-10T23:01:14Z"
},
{
"tag": "v0.15.1",
"kind": "patch",
"published_at": "2018-09-13T20:30:05Z"
},
{
"tag": "v0.15.0.1",
"kind": "other",
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"body": "Implement it via low-level code for str, bytes, and int.\nA small script was used to generate pysam_seq_comp_table:\n\n import pysam\n iupac = \"=ACMGRSVTWYHKDBN\"\n for c in range(256):\n\tif c % 16 == 0: print(\"\\n \", end='')\n\tbase = chr(c).upper()\n\tif base == 'U': base = 'T'\n\tif (b := iupac.find\n[…]\nomplement(b)]\n\t if chr(c).islower(): comp = comp.lower()\n\t print(f\" '{comp}', \", end='')\n\telse:\n\t print(f\" 0x{c:02x},\", end='')\n\nUse the new function in AlignedSegment.get_forward_sequence().",
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"headline": "Belated happy new year",
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"is_bot": false,
"headline": "Move the VCF/BCF documentation up alongside SAM/BAM/CRAM",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T08:59:29Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3f2aaf8e9eb20249745d012e77fb08d41328c235",
"body": null,
"is_bot": false,
"headline": "Rearrange Variant* class documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T08:33:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8a96ea0b91bb7327748cef5b7860631ed1de398f",
"body": null,
"is_bot": false,
"headline": "Further clarify VariantRecord properties documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T02:46:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8a9f7f8dd0aefdafb96262c4bdb4bd68d32ec2c7",
"body": "The filenames should also take pathlib.Path; VariantFile does not currently\nsupport file descriptors. HTSlib modes can include comma-separated format\noptions, so Literal is too limited and we should (TODO) remove pysam's\nruntime restrictions on this argument. Fixes #1405.",
"is_bot": false,
"headline": "Correct the AlignmentFile/VariantFile filename/mode type hints",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-26T07:05:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9aa4d1a1cd6eee0483c8f1fc45479f83705a3cdb",
"body": null,
"is_bot": false,
"headline": "Add documentation for all VariantHeader-related classes (PR #1394)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-25T22:36:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "48688fc3f4e2b7f58c1cdf250a2097833d142e87",
"body": "The data is contiguous so we can use [::1] to omit stride calculations.\nUsing explicit memoryviews rather than the previous array indexing code \nleads to a 100x speedup within this function.",
"is_bot": false,
"headline": "Use memoryviews to optimize array_to_qualitystring (PR #1363)",
"author_name": "Josh Chorlton",
"author_login": "jchorl",
"committed_at": "2026-04-17T10:08:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d12398616afaa3ca4f2ad86592dcabba74a4b1b0",
"body": null,
"is_bot": false,
"headline": "Add VariantContig and VariantMetadata documentation (PR #1361)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-12T12:49:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6aa975c485a2678d99c685698b6c53981c15eeb6",
"body": "Fixes #882; fixes #1368.",
"is_bot": false,
"headline": "Add documentation for all VariantRecord-related classes (PR #1359)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-12T01:27:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "427650a8bf5ff38eb6d035f8085d0e488df9ec67",
"body": null,
"is_bot": false,
"headline": "Adjust for FreeBSD py311-cython package name change",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-07T12:27:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7f508219393604218fab9b5e54715d9401bd339c",
"body": "Also remove setup-miniconda's unnecessary auto-activate-base override.",
"is_bot": false,
"headline": "Update to node24-based GitHub Actions",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-07T11:48:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a91efe36089dcdc1b2eebee2916643d68499cab6",
"body": "Mypy 1.20.0 was released today and reports types such as int\nas \"int\" rather than \"builtins.int\" as in previous versions.",
"is_bot": false,
"headline": "Handle mypy 1.20.0's changed output in typechecking testcases",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-01T10:54:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ec689af1918406185773b5a2cdf3645f6317ff6f",
"body": null,
"is_bot": false,
"headline": "Reformat get_tag() documentation to our usual NumPy style and tidy up",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-01T08:23:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "32752e938adc67c86d9f29c8d7b5c22ed6f3b151",
"body": "Apply similar changes as made previously to VariantRecordSample.update().",
"is_bot": false,
"headline": "Fix other update() methods with iterables and keyword args only",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-31T10:47:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ce2242855f83fdc8d57ee6033c46153e65fa46a4",
"body": "Add documentation for the class and its methods.\nFixes #407; fixes #720.",
"is_bot": false,
"headline": "Add VariantRecordSample documentation (PR #1358)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-03-31T09:15:16Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0f5a36a157f412d7ad943c7fdc148d14c2dc342a",
"body": "This is documented as accepting an iterable or solely keyword arguments,\nso check before using `items.items()`. Changing the default argument value\ncauses changes only within pysam/libcbcf.c, so has no ABI implications.",
"is_bot": false,
"headline": "Fix VariantRecordSample.update() with iterables and keyword args only",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-31T07:29:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2a3911171f3c6b3b4d907566cf0380edc77e7b62",
"body": "Link from the AlignmentFile(format_options) and HTSFile.add_hts_options()\nentries. Bring the AlignmentFile constructor signature docstring uptodate.",
"is_bot": false,
"headline": "Add link to samtools --input/output-fmt-option keyword documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-25T12:45:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a417ba16ef7c4bcb4bc08db86c6653a859388e65",
"body": "Add force_bytes() to convert the input str to bytes as hts_opt_add()\nis expecting.\n\nSimplify the function's signature by making format_options non-optional:\nthere is no point calling this function without specifying format_options,\nand [] is a more suitable no-op.\n\nSimplify the function's implementation by using `finally` for cleanup.\n(Both hts_opt_free() and hts_opt_apply() accept NULL as a no-op.)\nRaise ValueError rather than the more generic RuntimeError.",
"is_bot": false,
"headline": "Fix HTSFile.add_hts_options() str vs bytes handling",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-24T11:38:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4c50e83be0e787fe0c3dd179cc6dd4c32de50e75",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.23.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23.1\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23.1\n\nTake care to preserve these additional manual changes:\n\n* remov\n[…]\nom htslib/Makefile\n* the wheel-building PKI workaround in htslib/hfile_libcurl.c\n* the #define additions to bcftools/regidx.h\n\nand don't bother adding {sam,bcf}tools/htslib-1.23.1/{LICENSE,**/README}.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.23.1",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-19T07:00:23Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "54f3d41f380f095e8bfb16fd430b00fe02fb5063",
"body": "Regularise pysam/*.pyx directives to include `language_level=3` and exclude\n`profile=True`. Reactivate profiling if a PYSAM_PROFILE environment variable\nis set to a true value for both sdist and build_ext commands. Fixes #1350.\n\n(We could set `force` if PYSAM_PROFILE is set differently from the previous\nbuild, but it seems better to leave that to Cython's build_ext and require\nclean_ext when changing settings.)",
"is_bot": false,
"headline": "Update cython directives, turning profiling off by default",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-15T08:52:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e03c4e31dc8b6d2d3f1c81e3b666b4bf4f2a4dc7",
"body": "… HACK]\n\nLinux wheels are (currently) built on AlmaLinux, so the libcurl.so\nbundled into the wheel follows Alma/Red Hat/Fedora conventions for the\nlocation of its certificate bundle. This fails when the wheel is used on\na Debian/Ubuntu platform with a different convention for this location.\nWhen not\n[…]\nbian bundle location if the Red Hat one isn't present.\n\nReinstates b18dde87, which was inadvertently removed when importing 1.22.\nTake more care to preserve this patch when importing HTSlib in future!",
"is_bot": false,
"headline": "Fix wheels' bundled libcurl.so incompatibility with Debian [REINSTATE…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-09T07:36:03Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "79293854c45889bedef09491ee7d20de3dbc76a6",
"body": null,
"is_bot": false,
"headline": "Update cibuildwheel and use the new GH Actions case() function",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-31T06:04:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b7bf2cf7cb5e5263863d444223c63c150ec75eb2",
"body": null,
"is_bot": false,
"headline": "Update imports to htslib/samtools/bcftools 1.23 (PR #1372)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-12T07:31:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0a1997ea122541e6f00cc32f1dfa16a8fe42a820",
"body": "Remove pkg_resources, which is deprecated and slated for removal soon:\n_get_egg_name() has been unused since 2017 anyway.\n\nTake Extension from setuptools instead of distutils.\n\nUse sysconfig.get_config_var[s]() instead of distutils's wrappers.\nOverride LDSHARED properly in cy_build_ext.run() instead\n[…]\nig's own config_vars.\n\nThis linker_tests/link_pre_489/* test is unused anyway, and is present\nin the codebase for reference only. All of linker_tests/* deserves an\noverhaul; see also PR #489 and #503.",
"is_bot": false,
"headline": "Apply setup.py's modernisation to (unused) linker_tests/link_pre_489",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-11T09:34:39Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "0e05d9456fbd22432fa929b844eab7e442a0b992",
"body": "This symbol check is intended for detecting duplicate *pysam* symbols.\nIgnore any __pyx_* etc symbols, not just the particular function that\nCython 3.1.2 inadvertently left non-static, in case similar mistakes\noccur again in future.\n\nRemove the `License :: OSI Approved` classifier; License classifiers\nare apparently deprecated and cause warnings with recent setuptools.",
"is_bot": false,
"headline": "Generalise workaround for non-static Cython internal symbols",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-24T10:37:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "da8e5fee23ef9b30a3808fd331deb81d2281073c",
"body": "No longer need to be miserly with macOS actions runners, but continue to\nsuppress 3.8 to avoid a spurious error annotation. Update Python versions\nused for sdist and conda CI tests, and use newish setup-miniconda facility\nto suppress the defaults channel and avoid another annotation.\n\nBuild the release sdist on the latest Python release.",
"is_bot": false,
"headline": "Add Python 3.14 to CI and test most Python versions on macOS",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T18:22:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ac06a2152046806ed12c1d7e73ad728ac85b80eb",
"body": null,
"is_bot": false,
"headline": "Update pysam/libchtslib.pxd to HTSlib 1.23 htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T10:23:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "24c2b31cdbebd190f0bf36026e05015d2cf0a720",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.23\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.23/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.23",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T10:18:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "30475d23723df8ff19df6a20df1996d57df496bd",
"body": null,
"is_bot": false,
"headline": "Update Cirrus FreeBSD image (freebsd-14-2 is no longer available on GCP)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T09:33:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "caf56b2617472243e9a64a81de1a7f6846247703",
"body": null,
"is_bot": false,
"headline": "Update imports to htslib/samtools 1.22.1 and bcftools 1.22 (PR #1343)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-25T09:36:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3db05f9e7e8be9718cd8008af012010fba65f4c8",
"body": "Add Python 3.14 to release workflows and update cibuildwheel to a release\nthat uses 3.14-final. Use the new macos-15-intel image instead of macos-13,\nwhich is obsolete.\n\nReorganise the build matrix to separate the manylinux and musllinux jobs\nso they run in parallel.\n\nMove all wheel building to GitH\n[…]\ne's\ndefault Python can no longer run current cibuildwheel (which requires 3.11),\nso it is time to move the ARM wheels to be built on GitHub Actions, now that\nthat supports both Linux and macOS on ARM.",
"is_bot": false,
"headline": "Update release workflows for Python 3.14, Intel macOS runner, etc",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-22T06:04:37Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "d6fbe29d51049cee8adc23059f82885c01cb3ac5",
"body": "Store the output of `force_bytes(stdout_f)` in a live object to ensure\nit is not garbage-collected before it is used within samtools_dispatch().\nThis fixes a test failure on i386 (SamtoolsTest/PysamTest for calmd).",
"is_bot": false,
"headline": "Ensure stdout filename object is not garbage-collected while in use in C",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-17T05:41:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "23d81183ad9c00467bdafbb359abffada5797f15",
"body": null,
"is_bot": false,
"headline": "Update pysam/libchtslib.pxd to HTSlib 1.22.1 htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-15T07:23:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1de219ab4a66ee35e485e47e78ed659a6069bad7",
"body": "These tests fail on e.g. i386 because scalar types and layout differ\non this platform. Restrict the tests to run only on the common 64-bit\nplatforms -- we care mostly about incompatibilities on these platforms,\nand failures here will be generally indicative anyway. Fixes #1367.",
"is_bot": false,
"headline": "Run class size tests only on aarch64 and x86_64",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-14T22:50:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c4c0f8d5d50f8b8ed2ab39353029f480d0b7de17",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.22.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22.1\n\nTake care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools 1.22.1",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:54:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1190ab7e0c22a5fa63bcacd2f995a165b63c90ec",
"body": null,
"is_bot": false,
"headline": "Add new `samtools checksum` command",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a4a502880718b28a23ef999310933410cb360959",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.22\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.22\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.22/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.22",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "345625eb43bc3974c671f78a0097294a523053d3",
"body": "Omit the htslib/ref_cache/ source code, and hard-code a configure\n--disable-ref-cache argument accordingly.\n\nBCFtools's mpileup2/* is currently used only by plugins/vrfs.c which\nwe don't wrap, so we can (for now) omit this mpileup2/* code too.",
"is_bot": false,
"headline": "Don't import ref_cache/ external tool source code or mpileup2/*.[ch]",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bbad7c553341b63cace60bce0302e30094a2d7a7",
"body": null,
"is_bot": false,
"headline": "Update common GitHub Actions to their Node24-based versions",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-07T10:08:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6a78ccad576ae5b973998a9b25a0b8f84623b0eb",
"body": "These operate by adjusting for clipping, so when there is no CIGAR there\nis no adjustment from 0 and query_length. Documentation fixes #1319.",
"is_bot": false,
"headline": "Clarify query_alignment_start/_end/_length values for unmapped reads",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-16T07:09:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b59a459cfac40f74451ca4f5b29665057f159646",
"body": "Use bam_mods_recorded() to query how many mods may be returned\nby bam_next_basemod() and allocate accordingly. Fixes #1348.",
"is_bot": false,
"headline": "Remove AlignedSegment.modified_bases's limit on number of mods",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:38:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "529ec4289c628294c5cfbfc870d824d8861b16e5",
"body": "Cython 3.0 was released two years ago and is now available in the system\npackage repositories of all major distributions as well as via pip etc.\n\nThe `globals().update(getattr(CIGAR_OPS, \"__members__\"))` work-around for\nCython 3.1.0's non-global enumerator behaviour change in fact does not work\nwith Cython 0.x so 3.x is already required for pysam.",
"is_bot": false,
"headline": "Require Cython 3.x",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:21:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ea43c089e572ecbe914aa29fafb27c5fac2877bf",
"body": null,
"is_bot": false,
"headline": "Merge pysam/libchtslib.pxd declaration updates (PR #1362)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:03:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4f45505aed209254ccd8b0e5279de1416501f2f9",
"body": "Use the full form of source_suffix, which has long been supported,\nas the simple form produces a warning with recent Sphinx versions.",
"is_bot": false,
"headline": "Update to current Sphinx and ReadTheDocs theme",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-08T10:03:37Z",
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{
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"key": "wiki",
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"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": 59,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "at_risk",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"dangerous_workflow",
"packaging",
"pinned_dependencies",
"signed_releases",
"token_permissions"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 49,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 13,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 5,
"scorecard_aggregate": 4.9
},
"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 is not maximal on development and all release branches",
"points": 4.5,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "2 out of 2 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 1/27 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 27 contributing companies or organizations",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no workflows found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "no update tool detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow not detected",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "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": "No tokens found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "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; 2 could not be assessed (no resolved version, an unsupported ecosystem, or beyond the reported package list). 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_unassessed",
"params": {
"count": 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": 2,
"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": 12
},
"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": "moderate",
"name": "AI Readiness",
"value": 51,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "at_risk",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 32,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.59,
"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": "59 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 31.5,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 59,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "moderate",
"name": "Verify loop (build / test / typecheck)",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_pinned_dependencies"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 57,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
"doc/Makefile",
"htslib/Makefile",
"tests/cbcf_data/Makefile",
"tests/pysam_data/Makefile",
"tests/tabix_data/Makefile"
],
"has_devcontainer": false,
"has_linter_config": false,
"typecheck_configs": [
"pysam/py.typed"
],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile"
}
}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"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": "pysam/py.typed",
"points": 11,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "pysam/py.typed"
}
}
],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "good",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 75,
"inputs": {
"primary_language": "Cython",
"largest_source_bytes": 230215,
"source_files_sampled": 458,
"oversized_source_files": 56
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Cython with type-check config (pysam/py.typed)",
"points": 27,
"status": "partial",
"details": [
{
"code": "typecheck_config_language",
"params": {
"files": "pysam/py.typed",
"language": "Cython"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "56/458 source files over 60KB",
"points": 48.3,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 458,
"oversized": 56
}
}
],
"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": [
"Could not fetch pypi package 'pysam.libchtslib' from its registry"
],
"report_type": "repository",
"generated_at": "2026-07-21T20:30:14.249715Z",
"schema_version": "0.23.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/p/pysam-developers/pysam.svg",
"full_name": "pysam-developers/pysam",
"license_state": "standard",
"license_spdx": "MIT"
}