dsh-repro-audit 0.0.0-stage → 0.1.0

package/CHANGELOG.md

@@ -0,0 +1,63 @@
+# Changelog
+
+All notable changes to this project are documented here. The format follows
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project
+adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Fixed
+
+- `repro_check` resolves a saved manifest through `realpath` and rejects a
+  symlink that escapes the workspace (`PATH_ESCAPE`).
+- Malformed saved manifests (invalid JSON, `null`, or missing required arrays)
+  return `INVALID_MANIFEST` instead of throwing a `SyntaxError`/`TypeError`.
+- `repro_card` validates its manifest/drift inputs (including `null` and each
+  drift finding's expected/actual fields) and returns `INVALID_MANIFEST`/
+  `INVALID_INPUT` rather than crashing on malformed JSON.
+- The symlink-skipping test now creates a real symlink and asserts that it is
+  skipped (the previous assertion was unconditional `|| true`).
+- `package.json`, `jsconfig.json` and `tsconfig*.json` are no longer classified
+  as input data; a Node project therefore no longer suppresses the `no_data`
+  gap with its build configuration.
+- The `no_seed` gap now recognizes lowercase `.r` (and `.Rmd`/`.qmd`) scripts;
+  it previously matched only `.py` and uppercase `.R`.
+- Exclude the configured record store from the scan when it is inside the
+  project (the default `.repro-audit/` is also in the skip list); previously a
+  second manifest/drift check hashed its own records as added data.
+- Disable repository-local fsmonitor hooks for the read-only `git` calls: a
+  repository can configure `core.fsmonitor` to an executable, which `git status`
+  would run. `GIT_OPTIONAL_LOCKS=0` also keeps `git status` from refreshing the
+  index. A regression test asserts the hook is not executed.
+- Strip inherited `GIT_*` variables before spawning git, so `GIT_DIR`/
+  `GIT_WORK_TREE` from the host cannot redirect the evidence to another
+  repository; covered by a regression test.
+
+### Changed
+
+- Test count is now 24; the README and evaluation notes list the new failure
+  branches.
+
+## [0.1.0] - 2026-11-08
+
+First release: reproducibility evidence and drift detection.
+
+### Added
+
+- `repro_manifest`: bounded, read-only scan recording git commit/dirty state,
+  lockfiles, environment pins, data/figure/notebook hashes, seed literals and
+  runnable commands, plus gap severities and a reproducibility level.
+- `repro_check`: re-scan and compare — changed, missing and added artifacts —
+  with the level downgraded when recorded evidence no longer matches.
+- `repro_card`: Markdown report card + SARIF 2.1.0.
+- REP v1 integration: the manifest's artifacts are written as a valid
+  `ResearchRecord` with `Artifact` rows (code/env/data/seed/command/figure/
+  notebook) and the manifest itself alongside it.
+- Path containment, symlink skipping, file/depth/hash caps; `git` only via
+  fixed read-only arguments with a timeout.
+- 17 tests; manual scenario matrix in the README.
+
+### Notes
+
+- Metadata-level audit only: a manifest proves bytes existed, not that the
+  analysis is correct or that its command reproduces the figures.

package/LICENSE

@@ -0,0 +1,201 @@
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package/README-zh.md

@@ -0,0 +1,124 @@
+# dsh-repro-audit
+
+**别人能复现这项分析吗 —— 以及从你记录至今，有没有东西发生漂移？**
+
+*有界、只读的扫描：记录 commit、lockfile、环境、数据哈希、图表、seed 与运行命令；对照这份记录做漂移检查；生成可直接交给评审的报告卡。*
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
+[![Node](https://img.shields.io/badge/node-%5E22.19%20%7C%7C%20%3E%3D24.9-brightgreen.svg)]()
+
+[English](README.md) · 简体中文
+
+---
+
+## 它做什么
+
+- **`repro_manifest`** 扫描工作区中的一个项目并记录：git commit + 工作区脏状态、依赖 lockfile、环境版本固定（`.nvmrc`、`.python-version`、`pyproject.toml`、Dockerfile……）、输入数据哈希、图表哈希、notebook、显式随机种子（`random_state`、`np.random.seed`、`set.seed`、`torch.manual_seed`……）以及可运行命令（package.json scripts、Makefile targets、`run`/`reproduce`/`analysis` 入口脚本）。
+- **`repro_check`** 重新扫描并对比：**发生变化**或**消失**的产物都会成为一项发现 —— 因此清单生成后被修改过的数据文件也能被抓住。
+- **`repro_card`** 把证据渲染为 Markdown + SARIF 2.1.0，逐项列出缺口、严重级别和具体建议。
+
+级别：`reproducible`（没有 error/warning 级缺口）、`partial`（只有 warning）、`not_reproducible`（存在任何 error 级缺口或漂移）、`unknown`（保留）。
+
+## 它不做什么
+
+- **不执行代码。** 绝不运行项目代码；唯一的子进程是 `git rev-parse` 和 `git status`，带超时且不经 shell。
+- **不上传、不构建。** 它不抓取数据、不安装依赖，也不复现图表。
+- **不声称结论为真。** 清单只能证明这些字节曾经存在，不能证明分析正确或完整。
+- **没有 UI。** 只输出 JSON、Markdown 与 SARIF。
+
+## 缺口代码
+
+| 代码 | 严重级别 | 含义 |
+|---|---|---|
+| `no_git_commit` | error | 不是 git 仓库，或没有任何 commit |
+| `no_lockfile` | error | 未记录依赖 lockfile |
+| `no_run_command` | error | 未找到入口 |
+| `dirty_worktree` | warning | 存在未提交的改动；commit 无法描述这些文件 |
+| `no_seed` | warning | 存在脚本，但未找到 seed 字面量 |
+| `no_data` | warning | 项目中无输入数据文件 |
+| `no_environment` | warning | 未固定运行时/环境 |
+| `unhashed_data` | warning | 某个数据文件超出哈希上限 |
+| `no_figures` | info | 没有图表/表格产物 |
+| `scan_truncated` | warning | 达到文件数上限 |
+
+error 级缺口会把级别降为 `not_reproducible`；warning 会把级别降为 `partial`。
+
+## 工具
+
+### `repro_manifest`
+
+`{ path? }` → `{ ok, manifest, recordPath }`。该记录是一条合法的 REP `ResearchRecord`，其 `artifacts` 是代码/环境/数据/seed/命令/图表/notebook 证据。
+
+### `repro_check`
+
+`{ manifest | manifestPath, path? }` → `{ ok, drift }`。`manifestPath` 相对于工作区；`path` 是要重新扫描的项目（默认是工作区根目录）。
+
+### `repro_card`
+
+`{ manifest, drift? }` → `{ ok, markdown, sarif }`。
+
+### 错误码
+
+`INVALID_INPUT` · `NOT_FOUND` · `PATH_ESCAPE` · `NOT_A_DIRECTORY` · `INVALID_MANIFEST` · `STORE_ERROR`
+
+## 兼容性与安装
+
+| | |
+|---|---|
+| DeepSeek Harness | **`dsh-v0.2.1-rc.5`**（2026-11-08 实测）；peer `>=0.2.1-0 <0.3.0 \|\| >=0.2.2-0 <0.3.0` |
+| Node | `^22.19.0 \|\| >=24.9.0`（实测 `24.22.1`），仅 ESM |
+| Peer 依赖 | `@perrylink/dsh-research-core ^0.1.0`、`@deepseek-ai/cordis ^4.0.5-alpha.1`、`@deepseek-ai/dsh-tools`、`@deepseek-ai/schemastery ^3.18.5-alpha.1` |
+| 运行时依赖 | **零** |
+
+```sh
+dsh plugin --profile <name> add @perrylink/dsh-research-core dsh-repro-audit
+dsh --profile <name> --dump-config | grep dsh-repro-audit
+```
+
+## 配置
+
+| 键 | 默认值 | 含义 |
+|---|---|---|
+| `enabled` | `true` | `false` 时不挂载任何内容 |
+| `root` | `.repro-audit` | 清单与记录的根目录 |
+| `workspaceRoot` | `process.cwd()` | 项目路径必须解析到该目录内 |
+| `maxFiles` | `2000` | 每次扫描访问的文件数（超限会报告） |
+| `maxDepth` | `6` | 目录深度 |
+| `maxFileBytes` | `8388608` | 单文件哈希上限（更大的数据只记录为未哈希 + 缺口） |
+
+忽略的目录：`.git`、`node_modules`、`.venv`、`dist`、`build`、`target`、`__pycache__`、`coverage`、`.next`、各缓存目录、`.repro-audit`，以及配置的存储根目录（当其位于项目内时）。
+
+## 安全边界
+
+- 项目只读；记录写入 `root` 下。若存储目录位于被扫描的树内（默认的 `.repro-audit/`），该目录会被排除，因此清单不会把自己生成的记录也纳入。
+- 项目内的符号链接会被报告并跳过，绝不跟随。
+- 哈希上限用于防止内存暴涨；达到文件数上限时会报告，而不是静默忽略。
+- `git` 以固定的只读参数运行，5 秒超时，并启用 `windowsHide`；不经 shell。仓库本地的 fsmonitor hook 被禁用（`-c core.fsmonitor=false`），`GIT_OPTIONAL_LOCKS=0` 阻止 `git status` 刷新/写入索引；继承来的 `GIT_*` 变量会被清除，因此 `git -C <root>` 无法被重定向到另一个仓库。
+
+## 评测
+
+**24 个测试**：扫描（lockfile/数据/图表/seed/命令/运行时、跳过 `node_modules`、符号链接跳过但报告、项目配置不计为数据、小写 `.r` 脚本、文件数上限、排除自身存储、不执行 fsmonitor hook、忽略继承的 `GIT_*`）、清单级别（干净 → reproducible、无 seed → partial、无 git → not_reproducible、有未提交改动 → partial、空项目的缺口集合）、漂移（数据变化 + 图表缺失、干净重查）、运行时（合法 REP 记录、内联清单、带项目路径的已保存清单、拒绝格式错误的已保存清单并报 `INVALID_MANIFEST`、拒绝符号链接清单逃逸、路径逃逸）、tools（schema、manifest→check→card 端到端、失败分支、格式错误的 card 输入）、包契约。
+
+人工样例矩阵（不声称基准测试结果 —— 产物集合基于规则，而非学习得到）：
+
+| 场景 | 预期 | 覆盖 |
+|---|---|---|
+| 完整项目、干净工作树 | `reproducible`，0 个缺口 | 测试 |
+| 无 seed | `partial`，`no_seed` | 测试 |
+| 无 git | `not_reproducible`，`no_git_commit` | 测试 |
+| 有未提交改动 | `partial`，`dirty_worktree` | 测试 |
+| 清单生成后数据被修改 | 漂移 `changed`，`not_reproducible` | 测试 |
+| 图表被删除 | 漂移 `missing` | 测试 |
+| 刚记录的清单 | 漂移为空 | 测试 |
+
+## 已知限制（v0.1）
+
+- 只到元数据层面：不验证记录的命令是否真的能复现图表。
+- seed 通过字面量模式发现；经由配置文件或环境变量注入的 seed 会被漏掉。
+- 图表只做哈希，未与生成它的脚本关联（尚无溯源图）。
+- 大型数据文件只记录为“未哈希”（并记一个缺口），而不是流式处理。
+- 不识别 `.gitignore`：已被忽略但实际存在的文件，只要属于数据/图表/相应扩展名，仍会被哈希。
+
+## 许可
+
+Apache-2.0。运行时不含第三方代码。

package/README.md

@@ -1,3 +1,130 @@
-# Temporary Holding Version
+# dsh-repro-audit
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+**Would someone else be able to reproduce this analysis — and has anything drifted since you recorded it?**
+
+*A bounded, read-only scan that records the commit, lockfiles, environment, data hashes, figures, seeds and run commands; a drift check against that record; and a report card you can hand to a reviewer.*
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
+[![Node](https://img.shields.io/badge/node-%5E22.19%20%7C%7C%20%3E%3D24.9-brightgreen.svg)]()
+
+English · [简体中文](README-zh.md)
+
+---
+
+## What it does
+
+- **`repro_manifest`** scans a workspace project and records: git commit + dirty state, dependency lockfiles, environment pins (`.nvmrc`, `.python-version`, `pyproject.toml`, Dockerfile…), input-data hashes, figure hashes, notebooks, explicit random seeds (`random_state`, `np.random.seed`, `set.seed`, `torch.manual_seed`…) and runnable commands (package.json scripts, Makefile targets, `run`/`reproduce`/`analysis` entry scripts).
+- **`repro_check`** re-scans and compares: an artifact that **changed** or **disappeared** is a finding — so a data file edited after the manifest is caught.
+- **`repro_card`** renders the evidence as Markdown + SARIF 2.1.0, with every gap, its severity and a concrete suggestion.
+
+Levels: `reproducible` (no error/warning gap), `partial` (warnings only), `not_reproducible` (any error gap or drift), `unknown` (reserved).
+
+## What it does not do
+
+- **No execution.** Project code is never run; the only subprocesses are `git rev-parse` and `git status`, with a timeout and no shell.
+- **No upload, no build.** It does not fetch data, install dependencies, or reproduce figures.
+- **No truth claim.** A manifest proves these bytes existed; it does not prove the analysis is correct or complete.
+- **No UI.** JSON + Markdown + SARIF only.
+
+## Gap codes
+
+| Code | Severity | Meaning |
+|---|---|---|
+| `no_git_commit` | error | not a git repo, or no commit |
+| `no_lockfile` | error | no dependency lockfile recorded |
+| `no_run_command` | error | no entry point found |
+| `dirty_worktree` | warning | uncommitted changes; the commit does not describe the files |
+| `no_seed` | warning | scripts exist but no seed literal was found |
+| `no_data` | warning | no input data file in the project |
+| `no_environment` | warning | no runtime/environment pin |
+| `unhashed_data` | warning | a data file exceeded the hash cap |
+| `no_figures` | info | no figure/table output |
+| `scan_truncated` | warning | the file cap was reached |
+
+Error gaps make the level `not_reproducible`; warnings make it `partial`.
+
+## Tools
+
+### `repro_manifest`
+
+`{ path? }` → `{ ok, manifest, recordPath }`. The record is a valid REP `ResearchRecord` whose `artifacts` are the code/env/data/seed/command/figure/notebook evidence.
+
+### `repro_check`
+
+`{ manifest | manifestPath, path? }` → `{ ok, drift }`. `manifestPath` is workspace-relative; `path` is the project to re-scan (defaults to the workspace root).
+
+### `repro_card`
+
+`{ manifest, drift? }` → `{ ok, markdown, sarif }`.
+
+### Error codes
+
+`INVALID_INPUT` · `NOT_FOUND` · `PATH_ESCAPE` · `NOT_A_DIRECTORY` · `INVALID_MANIFEST` · `STORE_ERROR`
+
+## Compatibility & install
+
+| | |
+|---|---|
+| DeepSeek Harness | **`dsh-v0.2.1-rc.5`** (verified 2026-11-08); peer `>=0.2.1-0 <0.3.0 \|\| >=0.2.2-0 <0.3.0` |
+| Node | `^22.19.0 \|\| >=24.9.0` (tested `24.22.1`), ESM only |
+| Peers | `@perrylink/dsh-research-core ^0.1.0`, `@deepseek-ai/cordis ^4.0.5-alpha.1`, `@deepseek-ai/dsh-tools`, `@deepseek-ai/schemastery ^3.18.5-alpha.1` |
+| Runtime dependencies | **zero** |
+
+```sh
+dsh plugin --profile <name> add @perrylink/dsh-research-core dsh-repro-audit
+dsh --profile <name> --dump-config | grep dsh-repro-audit
+```
+
+## Configuration
+
+| Key | Default | Meaning |
+|---|---|---|
+| `enabled` | `true` | `false` mounts nothing |
+| `root` | `.repro-audit` | manifest + record root |
+| `workspaceRoot` | `process.cwd()` | project paths must resolve inside it |
+| `maxFiles` | `2000` | files visited per scan (over-limit reported) |
+| `maxDepth` | `6` | directory depth |
+| `maxFileBytes` | `8388608` | per-file hash cap (larger data is recorded unhashed + gap) |
+
+Ignored directories: `.git`, `node_modules`, `.venv`, `dist`, `build`, `target`, `__pycache__`, `coverage`, `.next`, caches, `.repro-audit`, plus the configured store root when it is inside the project.
+
+## Security boundaries
+
+- The project is read-only; records go under `root`. A store that lives inside
+  the scanned tree (the default `.repro-audit/`) is excluded from the scan, so
+  the manifest cannot include its own records.
+- Symlinks inside the project are reported and skipped, never followed.
+- Hash caps prevent memory blow-ups; the file cap is reported, not ignored.
+- `git` runs with fixed read-only arguments, a 5 s timeout and `windowsHide`; no shell.
+  Repository-local fsmonitor hooks are disabled (`-c core.fsmonitor=false`) and
+  `GIT_OPTIONAL_LOCKS=0` keeps `git status` from refreshing/writing the index;
+  inherited `GIT_*` variables are stripped so `git -C <root>` cannot be
+  redirected to another repository.
+
+## Evaluation
+
+**24 tests**: scanning (lockfiles/data/figures/seeds/commands/runtimes, `node_modules` skipped, symlinks skipped but reported, project config not counted as data, lowercase `.r` scripts, file cap, own store excluded, fsmonitor hook not executed, inherited GIT_* ignored), manifest levels (clean → reproducible, no seed → partial, no git → not_reproducible, dirty → partial, empty project gap set), drift (changed data + missing figure, clean re-check), runtime (valid REP record, inline manifest, saved manifest with project path, malformed saved manifests rejected with `INVALID_MANIFEST`, symlinked manifest escape rejected, path escape), tools (schemas, manifest→check→card end-to-end, failure branch, malformed card input), package contract.
+
+Manual sample matrix (no benchmark claimed — the artifact set is rule-based, not learned):
+
+| Scenario | Expected | Covered |
+|---|---|---|
+| complete project, clean tree | `reproducible`, 0 gaps | test |
+| no seed | `partial`, `no_seed` | test |
+| no git | `not_reproducible`, `no_git_commit` | test |
+| uncommitted change | `partial`, `dirty_worktree` | test |
+| data edited after manifest | drift `changed`, `not_reproducible` | test |
+| figure deleted | drift `missing` | test |
+| just-recorded manifest | drift empty | test |
+
+## Known limitations (v0.1)
+
+- Metadata-level only: it does not verify that the recorded command actually reproduces the figures.
+- Seeds are found by literal patterns; seeds injected via config files or environment variables are missed.
+- Figures are hashed but not linked to the script that produced them (no provenance graph yet).
+- Large data files are recorded unhashed (with a gap) rather than streamed.
+- No `.gitignore` awareness: ignored-but-present files are still hashed if they are data/figure/extensions.
+
+## License
+
+Apache-2.0. No third-party runtime code.

package/cordis.patch.yml

@@ -0,0 +1,18 @@
+# dsh-repro-audit bundle patch: mount the reproducibility tools.
+#
+# Every key below is a Config field (Schemastery schema); invalid values fail the
+# profile load loudly. The scan is read-only and bounded; the only subprocesses
+# are git rev-parse / git status.
+- insert:
+    - id: dsh-repro-audit
+      name: dsh-repro-audit
+      config:
+        enabled: true
+        root: .repro-audit
+        # Maximum files visited per scan (over-limit is reported, not ignored).
+        maxFiles: 2000
+        # Maximum directory depth.
+        maxDepth: 6
+        # Maximum bytes hashed per file; larger data files are recorded unhashed
+        # and reported as a gap instead of being silently skipped.
+        maxFileBytes: 8388608

package/lib/config.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Config schema and resolution for `dsh-repro-audit`.
+ * @module dsh-repro-audit/config
+ */
+import z from '@deepseek-ai/schemastery';
+/** Raw plugin config. */
+export interface Config {
+    enabled?: boolean;
+    /** Store/record root. */
+    root?: string;
+    /** Workspace root that project paths must stay inside. */
+    workspaceRoot?: string;
+    /** Maximum files visited per scan. */
+    maxFiles?: number;
+    /** Maximum directory depth. */
+    maxDepth?: number;
+    /** Maximum bytes hashed per file. */
+    maxFileBytes?: number;
+}
+/** Fully resolved config. */
+export interface ResolvedConfig {
+    readonly enabled: boolean;
+    readonly root: string;
+    readonly workspaceRoot: string;
+    readonly maxFiles: number;
+    readonly maxDepth: number;
+    readonly maxFileBytes: number;
+}
+/** Schemastery schema. */
+export declare const Config: z<Config>;
+/**
+ * Validate raw values and fill explicit defaults.
+ * @param config - raw plugin config.
+ * @returns the fully resolved config.
+ */
+export declare function resolveConfig(config?: Config): ResolvedConfig;
+//# sourceMappingURL=config.d.ts.map

package/lib/config.d.ts.map

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package/lib/config.js

@@ -0,0 +1,44 @@
+/**
+ * Config schema and resolution for `dsh-repro-audit`.
+ * @module dsh-repro-audit/config
+ */
+import path from 'node:path';
+import z from '@deepseek-ai/schemastery';
+/** Schemastery schema. */
+export const Config = z.object({
+    enabled: z.boolean().default(true),
+    root: z.string().default('.repro-audit'),
+    workspaceRoot: z.string(),
+    maxFiles: z.number().default(2000),
+    maxDepth: z.number().default(6),
+    maxFileBytes: z.number().default(8 * 1024 * 1024),
+});
+/** Throw unless the value is a positive safe integer. */
+function assertPositiveInt(name, value) {
+    if (!Number.isSafeInteger(value) || value <= 0)
+        throw new TypeError(`${name} must be a positive safe integer, got ${String(value)}`);
+}
+/**
+ * Validate raw values and fill explicit defaults.
+ * @param config - raw plugin config.
+ * @returns the fully resolved config.
+ */
+export function resolveConfig(config = {}) {
+    const root = config.root ?? '.repro-audit';
+    if (typeof root !== 'string' || root.trim() === '')
+        throw new TypeError('root must be a non-empty path');
+    const maxFiles = config.maxFiles ?? 2000;
+    const maxDepth = config.maxDepth ?? 6;
+    const maxFileBytes = config.maxFileBytes ?? 8 * 1024 * 1024;
+    for (const [name, value] of Object.entries({ maxFiles, maxDepth, maxFileBytes }))
+        assertPositiveInt(name, value);
+    return {
+        enabled: config.enabled ?? true,
+        root: path.resolve(root),
+        workspaceRoot: path.resolve(config.workspaceRoot ?? process.cwd()),
+        maxFiles,
+        maxDepth,
+        maxFileBytes,
+    };
+}
+//# sourceMappingURL=config.js.map

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