公开记录中等
软件健康报告模式 0.27.0 · 指标 1.13.0 · 2026-07-28 03:35 UTC
N283T / zsasa
High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings
N283T/zsasa 的健康指数为 100 分中的 63 分，处于「中等」区间。 其得分最高的类别是Vitality（82/100），最低的是Security（42/100）。 最近一次更新在今天。 近期的大部分工作由 1 位贡献者完成。
63
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。
63
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 | zsasa | 0.9.1 | - | 23 | 0 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？
82
开发活跃度
76良好
评分方式
| 36/36 | 推送新近度 — 最近一次推送于 0 天前 |
| 12.5/36 | 提交节奏 — 52 周中有 18 周有提交 |
| 18/18 | 提交量 — 最近一年 896 次提交 |
| 10/10 | OpenSSF Scorecard：Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
所用输入
| commits_last_year | 896 |
| human_commit_share | 1 |
| days_since_last_push | 0 |
| active_weeks_last_year | 18 |
发布纪律
90优秀
评分方式
| 27/27 | 有发布版本 — 已发布 24 个发布版本 |
| 36/36 | 发布时效 — 最近一次发布版本于 0 天前 |
| 27/27 | 发布节奏 — 约每 8 天发布一次 |
| 0/10 | OpenSSF Scorecard：Signed-Releases — Project has not signed or included provenance with any releases. |
所用输入
| releases_count | 24 |
| latest_release_tag | v0.9.1 |
| releases_from_tags | 否 |
| days_since_latest_release | 0 |
| mean_days_between_releases | 8 |
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？
51
流行度与采用
15危急
评分方式
| 14.6/60 | 星标 — 9 个星标 |
| 0/25 | 复刻 — 0 个复刻 |
| 0/15 | 关注者 — 1 位关注者 |
所用输入
| forks | 0 |
| stars | 9 |
| watchers | 1 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
社区健康
92优秀
评分方式
| 22.5/22.5 | README |
| 22.5/22.5 | 许可证 — 可识别的许可证（MIT） |
| 18/18 | CONTRIBUTING 指南 |
| 13.5/13.5 | 行为准则 |
| 0/7.2 | 议题模板 |
| 6.3/6.3 | PR 模板 |
所用输入
| has_readme | 是 |
| has_license | 是 |
| has_contributing | 是 |
| has_issue_template | 否 |
| has_code_of_conduct | 是 |
| has_pull_request_template | 是 |
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？
55
维护者韧性（巴士系数）
10危急
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 |
| 0/10 | OpenSSF Scorecard：Contributors — project has 0 contributing companies or organizations -- score normalized to 0 |
所用输入
| bus_factor | 1 |
| contributors_sampled | 1 |
| top_contributor_share | 1 |
议题与 PR 响应能力
82良好
评分方式
| 44.7/46.8 | 议题解决 — 96% 的议题已关闭 |
| 37.6/38.3 | PR 接受 — 已裁定的 PR 中 376/382 已合并 |
| 0/15 | OpenSSF Scorecard：Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
所用输入
| merged_prs | 376 |
| open_issues | 1 |
| closed_issues | 22 |
| issue_closed_ratio | 0.957 |
| closed_unmerged_prs | 6 |
所有权与托管责任
47存在风险
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 |
| 9.8/25 | 所有者影响力 — N283T 有 22 位关注者 |
| 17.5/25 | 既往记录 — 44 个公开仓库，账户约 2 年 |
所用输入
| followers | 22 |
| owner_type | User |
| is_verified | — |
| owner_login | N283T |
| public_repos | 44 |
| account_age_days | 995 |
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。
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 0 天前 |
| 20/20 | 版本历史 — 23 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 | zsasa |
| ecosystems | pypi |
| any_deprecated | 否 |
| min_days_since_publish | 0 |
工程质量
基础的工程与文档实践是否到位？
80
工程实践
66中等
评分方式
| 24/24 | CI 工作流 — 3 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 |
| 18/20 | OpenSSF Scorecard：CI-Tests — 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
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://n283t.github.io/zsasa/ |
| 10/10 | 仓库描述 |
| 10/10 | 主题标签 — 5 个主题标签 |
| 10/10 | Wiki |
所用输入
| topics | bioinformatics, python, sasa, structural-biology, zig |
| has_wiki | 是 |
| homepage | https://n283t.github.io/zsasa/ |
| 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？
42
安全态势
42存在风险
评分方式
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — 无数据 |
| 2.2/2.5 | CI-Tests — 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
| 0/2.5 | Contributors — project has 0 contributing companies or organizations -- score normalized to 0 |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 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 6 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 1/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 5/5 | Security-Policy — security policy file detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 0/7.5 | Vulnerabilities — 43 existing vulnerabilities detected |
所用输入
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 4.2 |
已排除计分（无数据或不适用）：branch_protection。 其余权重已重新归一化。
AI 就绪度
该仓库在多大程度上具备与 AI 编码代理协同开发与维护的条件？这是一枚独立的实验性徽章——权重为 0.0，因此单独呈现，不影响总体健康评分。
69
AI 代理上下文与指引
85优秀
评分方式
| 45/45 | 代理指令 — AGENTS.md |
| 0/15 | 机器可读文档（llms.txt） |
| 40/40 | 可读的提交历史 — 100 次人类提交中有 99 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 | 0.99 |
| agent_instruction_files | AGENTS.md |
| agent_instruction_max_bytes | 6,650 |
评分方式
| 18/18 | 一条命令的引导启动 — benchmarks/external/freesasa_batch/Makefile |
| 22/22 | 自动化测试 |
| 0/11 | Lint / 格式化配置 |
| 11/11 | 静态类型检查 — website/tsconfig.json |
| 10/10 | 可复现环境 — Dockerfile, Nix, lockfile |
| 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 |
| 2/10 | OpenSSF Scorecard：Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
所用输入
| has_nix | 是 |
| has_tests | 是 |
| lockfiles | package-lock.json, uv.lock |
| has_dockerfile | 是 |
| typed_language | 否 |
| bootstrap_files | benchmarks/external/freesasa_batch/Makefile |
| has_devcontainer | 否 |
| has_linter_config | 否 |
| typecheck_configs | website/tsconfig.json |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
面向模型的代码可读性
82良好
评分方式
| 27/45 | 可类型检查的代码 — Zig，已配置类型检查（website/tsconfig.json） |
| 55/55 | 可控的文件大小 — 采样的 70 个源文件中有 0 个超过 60KB |
所用输入
| primary_language | Zig |
| largest_source_bytes | 37,433 |
| source_files_sampled | 70 |
| oversized_source_files | 0 |
机器可读接口
40存在风险
评分方式
| 0/40 | API 模式（OpenAPI/GraphQL/proto） |
| 0/20 | MCP 服务器 |
| 40/40 | 可运行示例 — examples |
所用输入
| example_dirs | examples |
| has_mcp_signal | 否 |
| api_schema_files | — |
关键数据
9GitHub 星标
1贡献者
896最近 12 个月提交数
0距最近推送天数
24发布版本数
1巴士系数（bus factor）
1开放议题
npm, 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
- GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
- deps.dev does not index pypi:zsasa@0.9.1; advisories assessed against the repository dependency graph instead
更多细节
OpenSSF Scorecard 4.2 / 10
4.2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 |
| 不适用 | Branch-Protection | internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md |
| 9 | CI-Tests | 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/30 approved changesets -- score normalized to 0 |
| 0 | Contributors | project has 0 contributing companies or organizations -- score normalized to 0 |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 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 6 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 2 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 2 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 10 | Security-Policy | security policy file detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 0 | Vulnerabilities | 43 existing vulnerabilities detected |
直接依赖 7
| 注册表 | 软件包 | 版本约束 | 清单文件 |
|---|---|---|---|
| PyPI | numpy | >=1.24 | python/pyproject.toml |
| PyPI | cffi | >=1.15 | python/pyproject.toml |
| npm | @docusaurus/core | ^3.7 | website/package.json |
| npm | @docusaurus/preset-classic | ^3.7 | website/package.json |
| npm | prism-react-renderer | ^2.4 | website/package.json |
| npm | react | ^19.0 | website/package.json |
| npm | react-dom | ^19.0 | website/package.json |
全部依赖 未采集
本报告未能采集到解析后的依赖集合：GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
原始 JSON 报告 机器可读
{
"data": {
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"sasa",
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"Shell": 11856,
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"pushed_at": "2026-07-28T03:26:22Z",
"created_at": "2026-01-23T06:36:31Z",
"owner_type": "User",
"updated_at": "2026-07-28T03:26:21Z",
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"headline": "feat: add safe AlphaFold batch fast path (#399)",
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"headline": "fix: gate inline CCD parsing (#392)",
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"headline": "feat: add trajectory bitmask LUT modes (#387)",
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"headline": "fix: optimize multichain workflow parsing (#385)",
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"headline": "feat: allow batch thread overcommit (#384)",
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"headline": "docs: refresh benchmark website (#381)",
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"headline": "docs: recommend pyztraj for Python trajectory I/O (#379)",
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"headline": "test: cover batch jsonl and ffi concurrency (#376)",
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"body": "* docs: design file-first workflow batch\n\n* docs: plan file-first workflow batch\n\n* test: add workflow chain selection helper\n\n* refactor: reuse prepared batch SASA calculation\n\n* feat: process workflow batch files once\n\n* fix: preserve workflow auth-chain fallback\n\n* fix: honor workflow thread coun\n[…]\nkflow file-first outputs\n\n* test: exercise workflow file-first output layout\n\n* docs: note workflow job reuse\n\n* docs: clarify workflow reuse eligibility\n\n* fix: preserve long chain workflow filtering",
"is_bot": false,
"headline": "feat: reuse parsed inputs across workflow jobs (#374)",
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"headline": "fix: use inline CCD from BinaryCIF (#373)",
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{
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"body": "* docs: design binary cif input support\n\n* docs: plan binary cif implementation\n\n* feat: add binary cif messagepack reader\n\n* test: discover binary cif parser tests\n\n* feat: decode binary cif columns\n\n* fix: harden binary cif decoder errors\n\n* feat: parse binary cif atom site\n\n* fix: align binary ci\n[…]\n\n\n* feat: route binary cif inputs\n\n* test: add binary cif smoke coverage\n\n* docs: document binary cif input support\n\n* fix: handle masked binary cif columns\n\n* test: suppress workflow validation noise",
"is_bot": false,
"headline": "Add BinaryCIF input support (#372)",
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"body": "* feat: add adaptive bitmask batch mode\n\n* docs: document adaptive bitmask batch mode",
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"headline": "feat: add adaptive bitmask batch mode (#371)",
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"headline": "docs: restructure website docs (#370)",
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"headline": "release: v0.4.0 (#369)",
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"headline": "ci: ignore gitignore-only changes (#368)",
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"is_bot": false,
"headline": "chore: add agent instructions and ignore local docs (#367)",
"author_name": "N283T",
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"body": "* docs: design workflow manifest\n\n* docs: plan workflow manifest implementation\n\n* feat: add workflow manifest parser\n\n* fix: reject duplicate workflow manifest keys\n\n* fix: detect empty duplicate workflow sections\n\n* feat: require TOML custom classifiers\n\n* fix: tighten legacy classifier config rej\n[…]\nkflow classifier docs\n\n* fix: include workflow manifest read errors\n\n* test: add workflow smoke fixtures\n\n* fix: create calc workflow output directories\n\n* fix: honor calc classifier workflow override",
"is_bot": false,
"headline": "[codex] add workflow manifest support (#366)",
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"headline": "release: v0.3.2 (#365)",
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"body": "* docs: specify batch JSONL residue map\n\n* feat: add JSONL residue map serialization\n\n* feat: parse batch residue map option\n\n* feat: validate residue map JSONL format\n\n* feat: stream residue map JSONL rows\n\n* feat: build residue maps for batch results\n\n* docs: document batch residue map output\n\n* refactor: rename batch JSONL row helper",
"is_bot": false,
"headline": "[codex] Add batch JSONL residue map output (#364)",
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"headline": "release: v0.3.1 (#362)",
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"body": "* docs: design batch manifest\n\n* docs: plan batch manifest implementation\n\n* feat: parse manifest TOML values\n\n* fix: clean up TOML parser allocations\n\n* fix: clean up inline TOML values\n\n* feat: parse batch manifests\n\n* feat: parse batch manifest options\n\n* feat: filter batch inputs by chain\n\n* feat: run batch manifests\n\n* fix: validate batch manifest numeric options\n\n* fix: preserve CLI auth-chain override\n\n* docs: document batch manifests\n\n* docs: clarify batch manifest usage",
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"headline": "[codex] add batch TOML manifests (#361)",
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"oid": "36f3d9e8ed76cfa72470497820f4a8f56b796ac3",
"body": "## [0.3.0] - 2026-05-17\n\n### Added\n\n- **Zstandard decompression for structure inputs**: `.json.zst`, `.pdb.zst`, `.cif.zst`, `.mmcif.zst`, `.ent.zst`, `.sdf.zst`, and `.mol.zst` are now detected and transparently decompressed via native `std.compress.zstd`. (#357)\n\n### Changed\n\n- **CLI progress bars\n[…]\n` and `traj`, reducing custom rendering logic while preserving progress reporting. (#358)\n- **Project branding documentation**: add the project logo to README and refresh logo SVG assets. (#355, #356)",
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"body": "* docs: add CLI progress bars design\n\n* feat: use std progress for CLI progress bars\n\n* fix: let quiet mode override progress display",
"is_bot": false,
"headline": "[codex] use std progress for CLI progress bars (#358)",
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"oid": "a85e52fc2f9e36182fa5fca352e1ad9bd922cd56",
"body": "* feat: add zstd compressed input support\n\n* fix: allow exact decompression size limit",
"is_bot": false,
"headline": "[codex] add zstd compressed input support (#357)",
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"committed_at": "2026-05-15T10:10:56Z",
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"oid": "a08dc7db27005faef3579e68ce3f004f9594174a",
"body": "docs: update logo SVG assets",
"is_bot": false,
"headline": "Merge pull request #356 from N283T/codex/update-logo-svg",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-05-04T15:43:45Z",
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"is_bot": false,
"headline": "docs: update logo svg assets",
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"committed_at": "2026-05-04T15:43:18Z",
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{
"oid": "2ec53d9efeabfffb5894970d079cb426e4ed4472",
"body": "docs: add project logo",
"is_bot": false,
"headline": "Merge pull request #355 from N283T/codex/add-logo-readme",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-05-04T15:29:57Z",
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"headline": "docs: add project logo",
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"committed_at": "2026-05-04T15:29:29Z",
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"headline": "release: v0.2.11 (#354)",
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"committed_at": "2026-04-26T12:43:16Z",
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"oid": "e02b8cd68cc7d3bbb4ef42c0eb596d235f36d1a3",
"body": "The Build & Publish workflow has been silently broken since v0.2.9 because\nPR1 missed several Zig version pins outside build.zig.zon / flake.nix /\n.github/workflows/. v0.2.10's wheel/Docker publish surfaced these plus\ntwo follow-on issues.\n\nChanges:\n\n- **Bump Zig 0.15.2 → 0.16.0 in 9 files** missed \n[…]\neamTooLong errors on benign reads (broke\n the Windows wheel test for examples/1ubq.cif). For trusted local input\n files .unlimited is acceptable; mmapFile callers already trust the path.\n\nRefs: #342",
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"headline": "fix: clean up Zig 0.15.2 pins and Windows mmap reader regression (#353)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T12:36:54Z",
"body_truncated": true,
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{
"oid": "01a96229a483c444e3f005aec25a46f1d4e5ab85",
"body": "- Bump version in build.zig, build.zig.zon, python/pyproject.toml, python/uv.lock\n- Bump flake.nix derivation version from 0.2.4 → 0.2.10 (catches up the stale Nix derivation field that previous releases missed)\n- CHANGELOG entry for the gzip → native std.compress.flate revert (#351)\n\nRefs: #342",
"is_bot": false,
"headline": "release: v0.2.10 (#352)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T12:17:47Z",
"body_truncated": false,
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{
"oid": "3691a63be747ada9d816816e8803fce10f4a3725",
"body": "* fix: revert gzip to native std.compress.flate\n\nThe upstream panic (ziglang/zig#25035) that prompted #320's C-zlib workaround\nis fixed in Zig 0.16. Restore the native flate decompressor while preserving\nthe 4 GB decompression-bomb cap and the public API (readGzip / readGzipLimited\n/ DEFAULT_MAX_SIZ\n[…]\ns without\n.link_libc; on Linux the explicit flag is mandatory and removing it\nbroke the Linux jobs in CI for #351.\n\nThe CLI executable does not need libc — it uses GeneralPurposeAllocator.\n\nRefs: #342",
"is_bot": false,
"headline": "fix: revert gzip to native std.compress.flate (#351)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T12:06:16Z",
"body_truncated": true,
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{
"oid": "c323fd4a82fb379d981f73bd365a7518eb1c5290",
"body": "Implementation plan for reverting the C-zlib gzip workaround introduced\nin #320 back to native std.compress.flate. Covers the 3-commit sequence\nfrom the migration spec (rewrite gzip.zig, drop zlib from build.zig,\ndrop zlib from build.zig.zon) plus full verification matrix including\nthe 2oxd.cif.gz headline check.\n\nRefs: #342",
"is_bot": false,
"headline": "docs: add Zig 0.16 migration PR2 plan (#350)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T11:26:17Z",
"body_truncated": false,
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{
"oid": "aaa726c6f5dfce4e27823ae6c0b0c27154bd86f5",
"body": null,
"is_bot": false,
"headline": "release: v0.2.9 (#349)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T11:04:00Z",
"body_truncated": false,
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{
"oid": "9bb95928ac4d27f9564b8fa25c7e3a7c71f22038",
"body": "* chore: bump toolchain to Zig 0.16.0\n\n* refactor: introduce Io.Threaded in main and thread io through subcommands\n\nConstruct one std.Io.Threaded (.init_single_threaded) in main() and\nthread std.Io through to calc.run, batch.run, traj.run, and\ncompile_dict.run. Subcommand handlers accept io as a stu\n[…]\nexpand wrapper comment to explain why zlib_wrapper.h exists\n (addTranslateC requires b.path(), not a dependency lazy path)\n- src/c/zlib_wrapper.h: add one-line rationale comment referencing build.zig",
"is_bot": false,
"headline": "chore: migrate to Zig 0.16 (#345)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T10:53:45Z",
"body_truncated": true,
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},
{
"oid": "27729b29732ec5b4dd4f714330f3d663d61df617",
"body": "* docs: add Zig 0.16 migration design spec\n\nTwo-PR plan to migrate zsasa from Zig 0.15.2 to 0.16.0 (issue #342):\n- PR1: toolchain bump + 0.16 API migration\n- PR2: revert gzip C-zlib workaround to native std.compress.flate\n\nEach PR ships independently as a patch release.\n\n* docs: add Zig 0.16 migrati\n[…]\nontainer conversion, @cImport relocation, float-to-int audit,\nand verification (build/test/smoke matrix/python bindings).\n\nRefs #342, spec docs/superpowers/specs/2026-04-26-zig-016-migration-design.md",
"is_bot": false,
"headline": "docs: add Zig 0.16 migration spec and PR1 plan (#344)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T06:11:07Z",
"body_truncated": true,
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},
{
"oid": "8e52d97019d39f4c888d34a28b7e8882b97ad077",
"body": "fix: bump python/pyproject.toml to 0.2.8",
"is_bot": false,
"headline": "Merge pull request #341 from N283T/fix/release-version-sync",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T12:58:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "db0f334e19827abb877e26d38e2fb9bcba5a2053",
"body": "Was missed in the v0.2.8 release, causing PyPI publish to fail\n(wheels were built as 0.2.7, which already exists on PyPI).",
"is_bot": false,
"headline": "fix: bump python/pyproject.toml version to 0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T12:55:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ebe977d31458eef1dc6d29ac8b0f99d295dd98da",
"body": "release: v0.2.8",
"is_bot": false,
"headline": "Merge pull request #340 from N283T/release/v0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T05:28:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ac84e00aeb1284204d6f5f788f94214cced16828",
"body": "- SDF/MOL file support (V2000/V3000)\n- --sdf option for CCD-unregistered compounds\n- --mol option for molecule selection\n- Batch SDF expansion (per-molecule SASA)\n- ProtOr as CCD alias, Python CCD default\n- Memory safety fixes",
"is_bot": false,
"headline": "release: v0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:59:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d23483be880239efbe98fc32e125088df16a3459",
"body": "fix: process SDF molecules independently",
"is_bot": false,
"headline": "Merge pull request #339 from N283T/fix/sdf-per-molecule",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:54:07Z",
"body_truncated": false,
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},
{
"oid": "9588f651a82ebb089e4fc1dfac9bde1cad0cc95e",
"body": "- C1: Log warnings on SDF read/parse failures in buildWorkItems\n- I1+I2: Log warnings for toStoredComponent and dict allocation failures\n in processOneSdfMolecule instead of silently discarding errors\n- I3: Initialize result slot on double alloc failure in parallelWorker\n- I4: Free display_name str\n[…]\nlecules in selectMolecule\n- M3: Move doc comment to correct function (runBatchSequential)\n- M4: Warn when display name fallback to filename occurs\n- M5: Mention 1-based indexing in --mol error message",
"is_bot": false,
"headline": "fix: address review issues for SDF per-molecule processing",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:44:46Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "d2edf1c32fd9063be95bf081a61a0d14d65cb44c",
"body": "Multi-molecule SDF files previously combined all molecules into a single\nAtomInput (as chains A, B, C...), causing inter-molecule SASA interference.\n\ncalc: add --mol=NAME|N option to select a specific molecule; default to\nfirst molecule with a warning when multiple exist.\n\nbatch: expand each SDF fil\n[…]\n every molecule\ngets its own independent SASA calculation. Output files use stem_molname\nformat (e.g., two_molecules_water.json).\n\nsdf_parser: add test for single-molecule slice usage via toAtomInput.",
"is_bot": false,
"headline": "fix: process SDF molecules independently instead of as one structure",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:28:45Z",
"body_truncated": true,
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{
"oid": "6b1d6ba44144f7750b93e72e1a4ae593545a31a5",
"body": "feat: add SDF/MOL file support",
"is_bot": false,
"headline": "Merge pull request #338 from N283T/feature/sdf-support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:05:57Z",
"body_truncated": false,
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{
"oid": "b23a55467f5b76da73dbddb566a5afaf006a5825",
"body": "PR #337 changed the default classifier from NACCESS to CCD in\nPython bindings, but tests were not updated. Fix:\n- Update expected radii to CCD values (ALA:O 1.42, not 1.40)\n- Add explicit NACCESS classifier to NACCESS-specific tests\n- Add CCD-specific test for unknown residue behavior (returns None)",
"is_bot": false,
"headline": "fix: update Python classifier tests for CCD default",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T03:59:32Z",
"body_truncated": false,
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},
{
"oid": "11d53880291291a721a146960d05315a5977b1b9",
"body": "- C1: Fix toAtomInput over-allocation when >26 molecules by computing\n max_chains before the first-pass atom count\n- C2: Free StoredComponent on components.put failure in all locations\n- C3: Check for duplicate molecule names before inserting to avoid\n silent replacement and StoredComponent leak\n-\n[…]\nting double-free bug in parseSingleMolecule V3000 error\n path (errdefer freed name that parseV3000Body already owns)\n- Add tests: >26 molecules chain limit, V3000 bad bond index, bond\n order mapping",
"is_bot": false,
"headline": "fix: address critical and important issues from SDF PR review",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T03:52:20Z",
"body_truncated": true,
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},
{
"oid": "b077f976930c0009d3084356029cd27969203405",
"body": null,
"is_bot": false,
"headline": "docs: add SDF/MOL to supported input formats in README",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:40:11Z",
"body_truncated": false,
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},
{
"oid": "63bc9b270d14b3548aa3c154098158f50e958a29",
"body": "…traj\n\nAdd .sdf case to readInputFile in calc.zig and batch.zig, enabling\ndirect SDF file input with auto-format detection. Add --sdf=PATH CLI\noption to all three subcommands for loading external SDF bond topology\ninto the CCD classifier. SDF components from input files are\nauto-registered as CCD components (Task 9). The --sdf option can be\nspecified multiple times (up to 16 paths) and takes priority order:\nexplicit --sdf > auto-detected SDF > inline mmCIF > external CCD.",
"is_bot": false,
"headline": "feat: add SDF input support and --sdf CLI option to calc, batch, and …",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:36:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b6fc27254eded38ecdb02c94de2153aacb7ce9b7",
"body": "Add SDF and MOL file extensions to format detection so the system\ncan recognize .sdf, .sdf.gz, .mol, .mol.gz files (and uppercase\nvariants) and map them to the new `sdf` InputFormat variant.",
"is_bot": false,
"headline": "feat: add SDF/MOL format detection",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:27:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "16d66e8da766133ead440746d98b2bb3d653ca37",
"body": "Add two conversion functions to bridge SDF molecules with the CCD\nclassifier and SASA calculation pipeline:\n\n- toStoredComponent: converts SdfMolecule bond topology into a\n StoredComponent that the CCD classifier can use for hybridization\n analysis. Generates atom names as element+counter (C1, C2,\n[…]\nO1...).\n\n- toAtomInput: converts SDF molecules into AtomInput for SASA\n calculation. Each molecule maps to a separate chain (A-Z), with\n element VdW radii as defaults and optional hydrogen skipping.",
"is_bot": false,
"headline": "feat: add toStoredComponent and toAtomInput for SDF parser",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:25:53Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "9072e04c8ec3241cfc499a76ca39981346c854d2",
"body": "Replace the V3000 stub with a working parser that handles\nM V30 CTAB blocks including COUNTS, ATOM, and BOND sections.\nBond indices are converted from 1-based to 0-based with validation.",
"is_bot": false,
"headline": "feat: add SDF V3000 parser support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:22:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0eb3203a1f18b13d68ebbe742c378de4f0f112f2",
"body": "- Free name allocation on premature EOF return-null paths to prevent leaks\n- Separate toOwnedSlice calls with errdefer to prevent atoms leak if bonds fail\n- Use idiomatic try+orelse instead of catch-return for parseSingleMolecule\n- Extract sdfBondOrder helper for reuse in future V3000 parser",
"is_bot": false,
"headline": "fix: resolve memory safety issues in SDF parser",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:19:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "53070e608ba5a5e204706c73629c92525ada89b2",
"body": "Implements core SDF parser (sdf_parser.zig) with:\n- V2000 atom block parsing (coordinates + element symbols)\n- V2000 bond block parsing (1-based to 0-based index conversion)\n- Multi-molecule SDF support (separated by $$$$)\n- MOL file compatibility (single molecule without $$$$)\n- CRLF line ending handling\n- V3000 detection stub (returns error.InvalidV3000)\n- Comprehensive error handling and 7 embedded tests",
"is_bot": false,
"headline": "feat: add SDF/MOL parser with V2000 support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:13:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "beff839dbd074a0d0c1c0ace526299bb042a9e08",
"body": "…rmats",
"is_bot": false,
"headline": "test: add SDF test data files for V2000, V3000, and multi-molecule fo…",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:13:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4bbd6993f1fc1c8c5479a76ea86c0b57b64c80b1",
"body": "11-task plan covering:\n- SDF V2000/V3000 parser\n- Format detection\n- calc/batch/traj --sdf option\n- Auto CCD component registration for SDF input\n- Integration tests",
"is_bot": false,
"headline": "docs: add SDF support implementation plan",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:06:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c576e2df933922a93e152483d553aa9f03d211c6",
"body": "Design for two use cases:\n1. SDF as direct input file for SASA calculation\n2. --sdf option to provide bond topology for CCD-unregistered compounds",
"is_bot": false,
"headline": "docs: add SDF file support design spec",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:57:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "afd056a77780cbbff933adeaa504f4cca8446599",
"body": "feat: warn when --include-hydrogens used with CCD classifier",
"is_bot": false,
"headline": "Merge pull request #337 from N283T/feature/ccd-skip-hydrogens",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:39:20Z",
"body_truncated": false,
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},
{
"oid": "a9cdb555f84b22aa658becd20b6bcdcae39e7c7e",
"body": "MD trajectories typically contain explicit hydrogen atoms. CCD/ProtOr\nuse united-atom radii (implicit H), which causes double-counting with\nexplicit H. NACCESS handles explicit H via element fallback (H=1.10A).\n\n- Change traj default classifier from null to NACCESS\n- Update traj help text to explain the default\n- Update docs: Quick Recommendation shows per-command defaults\n- Simplify united-atom radii warning to recommend zsasa traj for MD",
"is_bot": false,
"headline": "feat: default traj classifier to NACCESS for MD trajectories",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:37:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fcdc1d518cf2c7dab57ff3eea67ce386107d7281",
"body": "CCD uses united-atom radii where heavy atom radii already account for\nimplicit hydrogens. Including explicit H atoms causes double-counting.\n\n- Add warning in calc.zig, batch.zig, traj.zig when CCD/ProtOr +\n --include-hydrogens is detected\n- Add docs warning about united-atom radii and explicit hydrogens\n- Document workarounds for MD trajectories with explicit H",
"is_bot": false,
"headline": "feat: warn when --include-hydrogens used with CCD classifier",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:34:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "621db008a8a835ca6f0e68cb63407cdb1c74fbc0",
"body": "docs: update classifier docs for ProtOr-CCD alias",
"is_bot": false,
"headline": "Merge pull request #336 from N283T/docs/protor-ccd-alias-update",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:34:25Z",
"body_truncated": false,
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},
{
"oid": "51b81e13b7fa7cdc9d8915c971a34ba92d79fd1a",
"body": "- CCD is now documented as default (not ProtOr)\n- ProtOr listed as alias for backward compatibility\n- Merge ProtOr/CCD Key Differences columns into single \"CCD (= ProtOr)\"\n- Update all code examples to use ClassifierType.CCD\n- Simplify CCD section intro (no longer contrasts with ProtOr)",
"is_bot": false,
"headline": "docs: update classifier docs to reflect ProtOr-CCD alias",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:27:24Z",
"body_truncated": false,
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},
{
"oid": "5b03d9e376d5593b9fd6f7b23e729c1826e8ab43",
"body": "refactor: make ProtOr an alias for CCD classifier",
"is_bot": false,
"headline": "Merge pull request #335 from N283T/refactor/protor-ccd-alias",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:25:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c648ddabe53b55ac0eeb54b24e85dec154b4a64b",
"body": "- Fix traj.zig parseClassifierType to use ClassifierType.fromString()\n (was hand-rolled parser that didn't accept \"ccd\")\n- Unify Python defaults to CCD across all modules:\n batch.py, biotite.py, biopython.py, gemmi.py\n- Fix calc.zig error message classifier ordering\n- Update c_api.zig constant comments (PROTOR = alias, CCD = default)",
"is_bot": false,
"headline": "fix: address review findings — traj parser, defaults, comments",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:24:51Z",
"body_truncated": false,
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},
{
"oid": "d4ea2fa4d513a94881f3aba39377c99232efd941",
"body": "ProtOr and CCD use identical radii for standard residues. CCD is a\nstrict superset that additionally handles non-standard residues via\nbond topology analysis. This removes the redundant classifier_protor.zig\nand routes all ProtOr lookups through CcdClassifier.\n\nChanges:\n- Delete src/classifier_proto\n[…]\nfrom protor to ccd\n- Update Python bindings default from NACCESS to CCD\n- HETATM auto-include remains ccd-only (no behavior change for protor users)\n- Update CLI help text and classifier documentation",
"is_bot": false,
"headline": "refactor: make ProtOr an alias for CCD classifier",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:17:51Z",
"body_truncated": true,
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},
{
"oid": "6460ee260163cbeee27c4baa0dd85bcef36c2d1c",
"body": "docs: rewrite CCD classifier section with accurate architecture",
"is_bot": false,
"headline": "Merge pull request #334 from N283T/docs/ccd-classifier-details",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:08:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "34f9f2c6f680709e2835d6fe200f0794dd2e5000",
"body": "\"most comprehensive\" → \"unique to zsasa\" to convey that the CCD\nclassifier is an original feature not found in other SASA tools.",
"is_bot": false,
"headline": "docs: clarify CCD classifier as unique to zsasa",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:08:10Z",
"body_truncated": false,
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},
{
"oid": "e401d98ba5d554080961122365bd162ae927f1c8",
"body": "- Fix \"zsasa's original classifier\" → \"most comprehensive\" (CCD is newest)\n- Fix residue count 37 → 45 with accurate grouping (selenoamino acids,\n PTMs, modified nucleotide PSU)\n- Split OONS C sp2 row: carbonyl (1.55, polar) vs aromatic (1.75, apolar)\n- Fix hybridization examples to match actual de\n[…]\nr uses element fallback for non-standard residues, CCD does not)\n- Add per-classifier residue support breakdown\n- Add PSU to nucleic acids section\n- Add rationale for CCD recommended vs ProtOr default",
"is_bot": false,
"headline": "docs: fix review findings — radii table, residue count, examples",
"author_name": "N283T",
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