Preserve CPU and GPU acceleration plans, evidence and LFS archives; mark research paused

2026-10-01 15:45:19 +08:00
parent 018f038c78
commit f2de879737
22 changed files with 19177 additions and 10 deletions
@@ -1,3 +1,4 @@
 # Preserve historical source bytes and SHA-256 across platforms. No EOL conversion.
 * -text
 *.jsonl.gz binary
+artifacts/acceleration-20261001/*.tar.zst filter=lfs diff=lfs merge=lfs -text
@@ -34,3 +34,5 @@ id_ed25519*
 /registry/verification-runs/
 # Historical learned deltas/checkpoints are not source files.
 /models/learned/
+# Explicit, audited experiment exports only; original data stay ignored.
+!/artifacts/acceleration-20261001/*.tar.zst
@@ -1,8 +1,23 @@
 # Digital Drosophila — 当前状态

-更新：2026-10-01。独立分支：`codex/lif-author-semantics-lab`。
+更新：2026-10-01。成果保存分支：`codex/v100-conditioning-acceleration`。

-## 最新状态（取代下方历史摘要的“当前／下一步”表述）
+## 最新状态：暂停研究，CPU/GPU 两套方案保留
+
+用户要求保存并上传现有成果，以后再继续。没有恢复训练、没有启动新实验，没有切换正式科学实现。
+
+- Phase 4AR 按真实已提交账本停在 **1,033/30,000 轮训练及 CPU 校验、138/3,920 probes**；末个未完成提交不算完成，也不自动重试。
+- 原科学登记 SHA 为 `b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740`，注册源码为 `80aeb2093db655329774eff7b32fb6e417b8b40b`。
+- CPU 原方案、独立 CPU 校验和常驻进程方案全部保留；GPU eligibility/update 原型在两张 V100 与 4090 的固定回放上通过逐位比较，没有替换原 CPU 代码。
+- 全脑常驻回放保持原 4090 环境、原始数学与 fresh state，42/42 次逐位一致。13 组稳态配对：原运行函数中位 5.9825 → 3.7222 秒，配对倍率中位 1.6201×；不是整轮训练加速，也不是学习成功。
+- 原实验 64,034 文件/16 源码、前一轮 659 产物/13 源码均保持一致。完整历史 Phase 1–4AQ 没有重跑。
+- 公开原始/参考数据已在独立 LFS 发布分支保存；本次另保存 CPU/GPU 科学回放结果，不包含环境、编译缓存或未确认许可的软件包。
+
+[CPU/GPU 方案、结果、恢复与限制](registry/acceleration-20261001/README.md) · [为什么有多个分支](docs/40-operations/branches-20261001.md)
+
+以下全部是历史状态，不能据此恢复任务或认为仍在运行。
+
+## 2026-10-01 00:09 的历史快照（已被上文停止状态取代）

 Phase 4AQ 已封存为 **PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。Phase 4AR 的普通嗅觉 acquisition 已登记并启动，仍在执行；学习成功尚未判定，没有新 learned candidate。

@@ -3,9 +3,9 @@
 面向 MaleCNS v1.0 的可审计连接组、LIF 模型、感觉接口与局部可塑性机制研究。
 **这是研究工程仓库，不是已经实现自主学习或游戏控制的果蝇。**

-截至 2026-10-01 00:09（Asia/Shanghai），最新封存阶段是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。
-**Phase 4AR 普通嗅觉 acquisition 正在执行，科学结论未判定**：采样时已提交 411/30,000 轮训练及 CPU 校验、62/3,920 次独立 probe；不是实时自动更新计数。
-最新研发分支为 `codex/lif-author-semantics-lab`，远端默认分支仍为初始化分支。本页状态不表示已完成分支合并。
+截至 2026-10-01，最新正式封存科学阶段仍是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。
+**Phase 4AR 已按用户要求停止，暂不恢复**：已提交 1,033/30,000 轮训练及 CPU 校验、138/3,920 次独立 probe；执行尚未完成，学习成功未判定。
+本分支 `codex/v100-conditioning-acceleration` 同时保留 CPU 与 GPU 方案及两轮独立性能回放。它不是已升级的生产运行时；原登记实验和权重没有改动。远端默认分支仍为初始化分支，见[分支说明](docs/40-operations/branches-20261001.md)。
 项目顶层验收口径为 **5/10（50%）**；这不是生物学逼真度、工作量完成率或剩余工期。
 最新正式候选运行时为 `MaleCNS-LIF-runtime-v2-deterministic-candidate`。
 `MaleCNS-TemporalEligibility-v2-candidate` 与 `MaleCNS-OlfactoryEncoder-v1-candidate` 保留。
@@ -15,7 +15,7 @@

 | 主题 | 文档 |
 |---|---|
-| 最新运行状态、证据与下一步 | [当前状态](CURRENT.md)、[本次同步说明](docs/progress/repository-sync-20261001.md) |
+| 最新运行状态、证据与下一步 | [当前状态](CURRENT.md)、[CPU/GPU 保存说明](registry/acceleration-20261001/README.md) |
 | 顶层验收比例与历史基线 | [项目状态](docs/00-overview/status.md) |
 | 目录和数据流 | [架构与目录](docs/00-overview/architecture.md) |
 | 科学数据定义和来源 | [数据契约](docs/10-data/data-contract.md)、[来源登记](docs/10-data/provenance.md) |
@@ -38,17 +38,17 @@

 服务器项目根目录：`/data/digital-drosophila/`。
 远程：`ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git`。
-初始化／当前远端默认分支：`codex/project-bootstrap`；最新研发分支：`codex/lif-author-semantics-lab`。
+初始化／当前远端默认分支：`codex/project-bootstrap`；注册科学源码分支：`codex/lif-author-semantics-lab`；最新独立加速成果：`codex/v100-conditioning-acceleration`。

 Git 保存源代码、配置、文档、书目、阶段证据副本和逐文件哈希清单。
-**Git 不保存原始 SWC/Feather、CSR、完整事件/状态、模型 checkpoint、虚拟环境或大型压缩包。**
+普通 Git 不直接保存大型科学二进制。获准公开再分发的原始/参考数据已在 `codex/lfs-public-resources` 通过 **Git LFS** 归档；本分支另通过 LFS 保存本次 CPU/GPU 回放的科学结果。没有上传虚拟环境、SDK 编译缓存、凭据或其他服务的数据。
 原项目实占约 29.72 GB（十进制、初始化前统计），不会因为初始化 Git 被删除、搬移或重写。
-仅 clone 本仓库不能恢复全数据；按[恢复说明](docs/30-reproducibility/restore.md)配置单独的数据副本。
+只取得 Git pointer 不能恢复全数据；需下载对应分支的 LFS 对象并验证内部成员。本次恢复说明见 [CPU/GPU 发布入口](registry/acceleration-20261001/README.md)。这不是全服务器灾备。

 ## 安全的首次检查

 ```bash
-git clone --branch codex/lif-author-semantics-lab ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
+GIT_LFS_SKIP_SMUDGE=1 git clone --branch codex/v100-conditioning-acceleration ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
 cd digital-drosophila
 python3 -B tools/repo_guard.py
 ```
@@ -0,0 +1,23 @@
+# 分支用途与当前入口
+
+2026-10-01 只读审计。此次只保存/推送已存在的加速实验分支，不删除分支、不强推、不合并、不更改默认分支。
+
+所有名称均带 `codex/` 前缀。
+
+| 分支 | 用途 |
+|---|---|
+| project-bootstrap | 最初项目归档、数据索引、论文与来源；当前远端默认入口 |
+| apl-pn-scope-audit | APL→PN 实际接触位置审计 |
+| terminal-scope-diagnostic | PN calyx 接触范围诊断 |
+| lif-semantics-audit | 冻结 LIF 语义与反馈回路审计 |
+| lif-author-semantics-lab | 独立模型及正式 Phase 4AR/CPU 实现，当前科学现场的分支 |
+| lfs-public-resources | 获准公开再分发的大数据、作者资源及实际远端恢复验证 |
+| v100-conditioning-acceleration | CPU 常驻、独立校验、V100 更新原型、4090 常驻回放；本次最新保存入口 |
+
+前五个主要是同一条提交历史上的阶段指针，并不是五份独立完整数据。它们线性继承至 `09187e4`，之后分为 LFS 资源发布和加速实验两条路线。Git/LFS 会按内容地址保存对象；多个分支名不意味着同一文件被完整复制多份。
+
+加速分支原已在本地存在，本次推送后远端共 7 个分支。CPU/GPU 两套实现放在同一加速分支的不同目录，不再各建分支。LFS 资源分支仍独立，不能把这次发布描述为已经合并全部数据。
+
+默认仍为最早的 bootstrap，所以网页默认看到的内容较旧。这是入口未整理，不是后续工作丢失。
+
+后续可在用户确认后统一主入口、给历史阶段打保留标签，再整理旧分支。集成 LFS 时需核对属性、状态文档、许可说明和自动下载开销；不得把工程实验分支直接视为通过科学验收的正式运行时。
@@ -0,0 +1,43 @@
+# CPU / GPU 方案保存 — 2026-10-01
+
+用户要求保存当前方案并上传，之后再继续。**原 Phase4AR 保持停止，未训练、未安装新权重，未进入下一科学阶段。**
+
+## 保存内容
+
+| 方案 | 代码 | 状态 |
+|---|---|---|
+| 原 CPU 更新与独立验证 | `models/male-cns-lif/olfactory-conditioning-lab-v1/`、`conditioning-interface-v2/` | 注册实现保留，未替换 |
+| V100/4090 eligibility 更新原型 | `models/male-cns-lif/conditioning-acceleration-v1/` | 固定案例逐位回放 PASS，不是全脑已迁移到 V100 |
+| CPU 常驻与 4090 全脑常驻 | `models/male-cns-lif/conditioning-pipeline-acceleration-v1/` | 42 次全脑精确回放 PASS，不是已验收生产运行时 |
+
+本目录的 `gpu/`、`pipeline/` 保存原报告、manifest 与完整性说明的原字节副本；`publication-catalog.json` 逐项记录公开归档成员和有意排除项。完整数值回放、请求、状态和诊断回执封装在 `artifacts/acceleration-20261001/` 的两个 Git LFS 归档中。
+
+代码版本：GPU 核心 `221e1f13f758ebe8d9f188bab976c361f7cacf45`；常驻回放封存 `018f038c7857c7e0236dd7408a680458520d92ce`。原科学登记源码 `80aeb2093db655329774eff7b32fb6e417b8b40b` 不变。
+
+原科学现场停在 1,033 轮已提交且 CPU 校验的训练、138 个已提交 probe。完整科学执行、独立学习 gate 未完成；本次性能成果不代表学会关联记忆。
+
+## 来源、许可与排除
+
+MaleCNS v1.0 原数据来源为 [官方数据页](https://male-cns.janelia.org/download/)，既有许可审计为 CC BY 4.0。署名保留 Male CNS collaboration：FlyEM/HHMI Janelia、University of Cambridge、MRC Laboratory of Molecular Biology、Google Research 及原论文作者。本项目进行了既有 neuron-only 过滤/重编号和模型模拟；本次只原字节复制已生成的回放数据，不重新推导或修改科学数值。
+
+嗅觉输入来源链中的 DoOR.data 2.0.1（commit `eea72d64b42a4e91dafe822cf0b5204de33f8d34`）维持 CC BY-SA 4.0，作者 Daniel Münch、C. Giovanni Galizia、Shouwen Ma、Martin Strauch、Anja Nissler。涉及其派生输入的成员保留此 ShareAlike/署名约束；不将其许可泛化至无关代码。[DoOR 论文](https://doi.org/10.1038/srep21841)。Shiu 作者源码维持其原 MIT 声明；本项目是 adapted dynamics，不是严格原模型复现。
+
+原资源许可证据及上游 notices 在 `codex/lfs-public-resources` 的 `registry/publication-20261001/`，固定发布提交 `5b1d1b7`。本次没有打包 NVIDIA SDK、CuPy/PyTorch 环境、FlyVis、论文全文或其他服务。软件没有被擅自统一换证，仍适用仓库 NOTICE 和各上游声明。
+
+明确排除：虚拟环境、CUDA 编译缓存/中间产物/二进制、安装下载日志。完整原实验（包括失败与编译诊断）仍原样留在服务器；原 sealed manifest 包含未上传缓存的哈希。因此公开归档应使用 **publication-catalog.json** 校验，不能要求原始全目录 SHA 清单在省略缓存的副本中全部通过。没有丢弃科学失败案例。
+
+旧原始/参考大数据不重复上传，它们在 `codex/lfs-public-resources`。本次发布不是全服务器或全部历史科学目录灾备，也没有打包已停止 AR 的所有 64,034 个现场文件。
+
+## 恢复与验证（不运行模型）
+
+在新目录 clone 本分支，安装 Git LFS，执行：
+
+```sh
+git lfs pull --include='artifacts/acceleration-20261001/**'
+python3 -B tools/acceleration-publication/archive_results.py verify
+```
+
+验证器只读流式校验归档 SHA、成员集合、每个成员字节数与 SHA，不解包、不运行模型。
+如需解包，只解到新建空目录；不得覆盖 `/data/digital-drosophila` 或直接运行旧封存脚本。性能原型依赖固定科学源与历史输入，不能只 clone 就自动恢复正式训练。
+
+`delivery.json` 只在真实远端 push、独立新 LFS store 下载和完整成员验证成功后写入。没有该回执时，不能把打包完成称为异机恢复已通过。
@@ -0,0 +1,29 @@
+# V100 conditioning acceleration — engineering replay result
+
+Status: **PASS-ELIGIBILITY-UPDATE-REPLAY-EQUIVALENCE**. This is not a learning result or a production-training promotion.
+
+Benchmark code commit: `221e1f13f758ebe8d9f188bab976c361f7cacf45`.
+
+| Device | Real-fixture replay median (prep + transfers + comparison) | Resident CUDA kernel median |
+|---|---:|---:|
+| Tesla V100-SXM2-16GB (v100a-02) | 3.430 ms | 0.122 ms |
+| Tesla V100-SXM2-16GB (v100b-01) | 3.344 ms | 0.122 ms |
+| NVIDIA GeForce RTX 4090 (rtx4090-01) | 3.327 ms | 0.074 ms |
+
+Each GPU passed14sealed real fixtures +16fixed synthetic cases, with sampled trace, final trace, allUS snapshots and delta byte-identical to the original independent CPU oracle. Six invalid inputs were rejected on each GPU.
+
+CPU warm reference includes the original API's repeated provenance checks and AST parsing; it is only one warm sample perfixture. GPU authenticates the source and complete anatomical mapping once. Therefore ratios in JSON describe API implementation replay, not pure hardware acceleration.
+
+The CUDA kernels preserve every timestep, float32 separate round-to-nearest operations, exact US timing, noUS zeros, compartment/frozen/D0 identity and the depression floor. No gain/learning-rate/tau/threshold/connectome/sign changes. No dense time×neuron matrix.
+
+A new candidate-only CuPy environment and explicit CUDA12.6 nvcc compilation are used. Original science and ComfyUI environments are unchanged. All three ComfyUI queues were checked before each fixture; no services were stopped.
+
+Integrity: 64034 saved files, 3103901058 bytes, 16 registered source files checked; no mismatch. This is the saved Phase4AR inventory, not a new Phase1–4AQ numerical regression.
+
+Phase4AR remains stopped at1033/30000CPU-verified epochs and138/3920probes. No weights were installed and no training was resumed.
+
+Next: a separately validated persistent-worker pipeline and end-to-end benchmark. This local optimization does not justify dividing the9-day estimate by the kernel speedup. Independent-seed V100 parallelism is not yet measured.
+
+Preserved failures: candidate packaging incompatibility (--report unsupported bypip22); first CuPy compile FTZ flag conflict (before any kernel ran). Both were corrected only in the independent branch.
+
+Compiler references: [CuPy precompiled RawModule](https://docs.cupy.dev/en/v13.6.0/reference/generated/cupy.RawModule.html), [CUDA12.6 compiler options](https://docs.nvidia.com/cuda/archive/12.6.3/cuda-compiler-driver-nvcc/index.html).
@@ -0,0 +1,660 @@
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+    "original_experiment_resumed": false,
+    "original_git_head": "09187e4d4d67badf1b418c5f211258ca5d8fb328",
+    "original_git_status": "",
+    "probes_completed_unchanged": 138,
+    "registered_science_commit": "80aeb2093db655329774eff7b32fb6e417b8b40b",
+    "registration_sha256": "b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740",
+    "scope": "Saved Phase4AR experiment/control files and registered source files; NOT a new Phase1-4AQ numerical regression",
+    "source_mismatches": [],
+    "sources_checked": 16,
+    "status": "PASS",
+    "training_epochs_cpu_verified_unchanged": 1033,
+    "wall_seconds": 4.8638160139998945
+  },
+  "full_brain_gpu_event_equivalence_tested": false,
+  "full_training_acceleration_measured": false,
+  "learned_candidate_created": false,
+  "limitations": [
+    "Replay module only, not a production training backend",
+    "The sampled committed prefix covers7arms but only available physiological/PAM15/reinforce_A subset",
+    "Repeated kernel calculations reset state and replay identical saved inputs, not additional learning trials",
+    "Original CPU verification remains independent and required",
+    "No simultaneous two-V100 training/scheduling benchmark; devices tested separately",
+    "Original9.07-day estimate is not replaced by this component benchmark"
+  ],
+  "next_work": "Separately validate persistent training/update/verification workers and complete chain timing before authorizing a new scientific execution version",
+  "original_experiment_resumed": false,
+  "report_code_commit": "221e1f13f758ebe8d9f188bab976c361f7cacf45",
+  "scientific_experiment_status": "STOPPED, unchanged:1033/30000 CPU-verified training epochs and138/3920 probes",
+  "status": "PASS-ELIGIBILITY-UPDATE-REPLAY-EQUIVALENCE",
+  "weights_installed": false
+}
@@ -0,0 +1,21 @@
+{
+  "catalog_sha256": "28071f276848ea60149f21a9794653486b404670a58b34d97b1aaae742095245",
+  "groups": {
+    "gpu": {
+      "archive_bytes": 1679158,
+      "files": 614,
+      "original_bytes": 13242628,
+      "sha256": "50acdc85342a2c79c3516e50ee4542b909813d179518451edaaf2d94150c534b",
+      "verified": true
+    },
+    "pipeline": {
+      "archive_bytes": 74767927,
+      "files": 1066,
+      "original_bytes": 103062185,
+      "sha256": "fdc39013d71fb7d14313d8249c929601a8a7050cc2eac88b733d692bbe1b6b42",
+      "verified": true
+    }
+  },
+  "pass_all": true,
+  "verification": "Full streamed members, no extraction or model execution"
+}
@@ -0,0 +1,31 @@
+# 常驻进程工程回放结果
+
+状态：`PASS-PERSISTENT-REPLAY-EQUIVALENCE`。仅限这次固定回放，不代表学习成功或正式运行时升级。
+
+## 实测
+
+| 测量范围 | 新进程 | 常驻进程 | 说明 |
+|---|---:|---:|---|
+| 原始 CPU 更新 API | 1.3480 s | 0.1182 s | 新进程首次 API 包含导入等开销 |
+| 完整更新 API，同一固定案例 | 3.7089 s | 2.3424 s | 仅一组冷启动对照 |
+| 全脑原始运行函数，13 组配对中位数 | 5.9825 s | 3.7222 s | 含原有输出；排除固定首例的初始化 |
+
+完整更新常驻 14 组中位耗时：2.3483 s。
+完整独立验证仍需：3.6435 s（14 组中位数）。
+全脑运行函数同案例配对倍率中位数：1.620×，不是整轮训练加速倍率。
+
+## 一致性与保护
+
+- 17 项主机测试通过。
+- CPU：14 次冷启动更新、42 次独立双进程更新/重算、29 次完整更新、14 次完整独立验证通过。
+- 全脑：14 次新进程、正序 14 次与逆序 14 次常驻回放；所有脉冲、状态、延迟队列和请求等一致，10 个数组逐位相同。
+- 64,034 个原实验文件与 16 个注册源码重新校验通过；之前 659 个加速产物和 13 个源码保持不变。
+- 原 Phase4AR 仍停止于 1,033 轮 CPU 校验训练与 138 次 probe，没有新增训练或安装新权重。
+
+## 边界与下一步
+
+本次全脑测试使用原 RTX 4090 环境，没有证明全脑已能迁移到 V100。此前 V100 约 3.4 ms 的成绩仅属于 eligibility/update 模块。
+常驻进程复用的是解释器、模块和 CUDA 上下文；每轮神经状态仍由原始函数重新分配。
+当前仍保留完整验证、图和权重上传、记录写盘。下一步应在新的可审计流水线中验证整轮开销，不能把本报告的独立阶段相加当作实测训练速度。
+
+源码提交：`018f038c7857c7e0236dd7408a680458520d92ce`。完整逐例耗时、实际进程退出、来源校验见 `final-summary.json` 和各 lane 报告。
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+      "original_git_head": "09187e4d4d67badf1b418c5f211258ca5d8fb328",
+      "original_git_status": "",
+      "probes_completed_unchanged": 138,
+      "registered_science_commit": "80aeb2093db655329774eff7b32fb6e417b8b40b",
+      "registration_sha256": "b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740",
+      "scope": "Saved Phase4AR experiment/control files and registered source files; NOT a new Phase1-4AQ numerical regression",
+      "source_mismatches": [],
+      "sources_checked": 16,
+      "status": "PASS",
+      "training_epochs_cpu_verified_unchanged": 1033,
+      "wall_seconds": 5.062658503000421
+    },
+    "original_AR_resumed": false,
+    "previous_engineering_files_checked": 659,
+    "previous_engineering_sources_checked": 13,
+    "previous_manifest_sha256": "6efdec34c96cdc79f786b91bd7a99b0e8ef64d0c4dcfa525646c82659a77d44f",
+    "status": "PASS",
+    "wall_seconds": 5.197849371999837
+  },
+  "jobs": {
+    "brain-replay-01": {
+      "command": [
+        "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
+        "-B",
+        "/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif/conditioning-pipeline-acceleration-v1/brain_replay.py",
+        "--fixtures",
+        "/home/qishizhe/phase4ar-v100-acceleration-20261001/fixtures",
+        "--fixture-manifest-sha256",
+        "481df128d39bf28e5984a6f2e5757f83d45cb7a6136f8d2843ecc0a67eca437b",
+        "--output",
+        "/home/qishizhe/phase4ar-pipeline-acceleration-20261001/brain-replay"
+      ],
+      "exit_code": 0,
+      "finished_utc": "2026-10-01T07:17:05.441907+00:00",
+      "label": "brain-replay-01",
+      "observed_exit": true,
+      "pid": 35046,
+      "process_group": 35046,
+      "scientific_AR_resumed": false,
+      "scope": "independent engineering replay only",
+      "started_utc": "2026-10-01T07:11:17.781251+00:00",
+      "stop_reason": null,
+      "timed_out": false,
+      "wall_seconds": 347.66065984800025
+    },
+    "brain-unit-tests": {
+      "command": [
+        "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
+        "-B",
+        "-m",
+        "unittest",
+        "discover",
+        "-s",
+        "/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif/conditioning-pipeline-acceleration-v1",
+        "-p",
+        "test_brain_replay.py",
+        "-v"
+      ],
+      "exit_code": 0,
+      "finished_utc": "2026-10-01T07:08:49.205842+00:00",
+      "label": "brain-unit-tests",
+      "observed_exit": true,
+      "pid": 34762,
+      "process_group": 34762,
+      "scientific_AR_resumed": false,
+      "scope": "independent engineering replay only",
+      "started_utc": "2026-10-01T07:08:49.035004+00:00",
+      "stop_reason": null,
+      "timed_out": false,
+      "wall_seconds": 0.17084325300038472
+    },
+    "cpu-profile-01": {
+      "command": [
+        "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
+        "-B",
+        "/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif/conditioning-pipeline-acceleration-v1/profile_original.py",
+        "--fixtures",
+        "/home/qishizhe/phase4ar-v100-acceleration-20261001/fixtures",
+        "--fixture-manifest-sha256",
+        "481df128d39bf28e5984a6f2e5757f83d45cb7a6136f8d2843ecc0a67eca437b",
+        "--output",
+        "/home/qishizhe/phase4ar-pipeline-acceleration-20261001/cpu-profile",
+        "--repeats",
+        "3"
+      ],
+      "exit_code": 0,
+      "finished_utc": "2026-10-01T07:08:22.538896+00:00",
+      "label": "cpu-profile-01",
+      "observed_exit": true,
+      "pid": 27868,
+      "process_group": 27868,
+      "scientific_AR_resumed": false,
+      "scope": "independent engineering replay only",
+      "started_utc": "2026-10-01T07:05:31.857063+00:00",
+      "stop_reason": null,
+      "timed_out": false,
+      "wall_seconds": 170.68183461700028
+    },
+    "cpu-unit-tests": {
+      "command": [
+        "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
+        "-B",
+        "-m",
+        "unittest",
+        "discover",
+        "-s",
+        "/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif/conditioning-pipeline-acceleration-v1",
+        "-p",
+        "test_profile_original.py",
+        "-v"
+      ],
+      "exit_code": 0,
+      "finished_utc": "2026-10-01T07:01:44.742692+00:00",
+      "label": "cpu-unit-tests",
+      "observed_exit": true,
+      "pid": 27719,
+      "process_group": 27719,
+      "scientific_AR_resumed": false,
+      "scope": "independent engineering replay only",
+      "started_utc": "2026-10-01T07:01:44.577624+00:00",
+      "stop_reason": null,
+      "timed_out": false,
+      "wall_seconds": 0.165072402000078
+    }
+  },
+  "limitations": [
+    "Fixed 14 real committed-prefix fixtures only; not the full scientific design.",
+    "Fresh means fresh interpreter, not flushed filesystem caches.",
+    "Brain uses unchanged original 4090 runtime; whole-brain V100 compatibility remains unestablished.",
+    "Original GPU tensors/graph are still allocated and uploaded each trial; no numerical loop rewrite.",
+    "Brain runtime timings include its original output I/O. Trial wall also includes extra audit checks.",
+    "Resident trial audit additionally checks the current fresh reference, making trial-wall boundaries unequal.",
+    "Paired steady timing excludes fixed fixture 0 cold initialization in both lanes; correctness excludes none.",
+    "Independent measured stages are not a combined training pipeline; no end-to-end speedup or revised full-run ETA.",
+    "Full independent AQ still uses a fresh subprocess and all original checks.",
+    "The original stopped scientific run remains at 1033 CPU-verified epochs and 138 probes.",
+    "Integrity covers saved Phase4AR files/sources and previous acceleration files; not a new Phase1-4AQ numerical regression.",
+    "Expected timeout self-test intentionally exits nonzero; it is not a scientific-run failure."
+  ],
+  "original_source_commit": "80aeb2093db655329774eff7b32fb6e417b8b40b",
+  "probes_added": 0,
+  "production_runtime_promoted": false,
+  "registration_sha256": "b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740",
+  "scientific_AR_resumed": false,
+  "scientific_learning_success_claimed": false,
+  "source_commit": "018f038c7857c7e0236dd7408a680458520d92ce",
+  "status": "PASS-PERSISTENT-REPLAY-EQUIVALENCE",
+  "training_epochs_added": 0
+}
@@ -0,0 +1,183 @@
+"""Read-only source packing and streamed verification for exact replay evidence."""
+import argparse
+from datetime import datetime, timezone
+import hashlib
+import io
+import json
+from pathlib import Path
+import re
+import shutil
+import subprocess
+import tarfile
+
+SOURCE_CODE = Path('/home/qishizhe/digital-drosophila-v100-acceleration/models/male-cns-lif')
+GROUPS = {
+    'gpu': (Path('/home/qishizhe/phase4ar-v100-acceleration-20261001'),
+            '6efdec34c96cdc79f786b91bd7a99b0e8ef64d0c4dcfa525646c82659a77d44f',
+            'conditioning-acceleration-v1'),
+    'pipeline': (Path('/home/qishizhe/phase4ar-pipeline-acceleration-20261001'),
+                 '4c598f51e927b3145891db42d9bb345c52d4aaa3b3a05ac257b207fff90cace4',
+                 'conditioning-pipeline-acceleration-v1'),
+}
+REGISTRY = Path('registry/acceleration-20261001')
+ARTIFACTS = Path('artifacts/acceleration-20261001')
+INSTALL_LOGS = {
+    'create-venv.stdout.log', 'create-venv.stderr.log',
+    'install-candidate.stdout.log', 'install-candidate.stderr.log',
+    'install-candidate-attempt-02.stdout.log', 'install-candidate-attempt-02.stderr.log',
+    'upgrade-candidate-pip.stdout.log', 'upgrade-candidate-pip.stderr.log',
+}
+SECRET_RULES = [
+    rb'-----BEGIN (?:OPENSSH |RSA |EC )?PRIVATE KEY-----',
+    rb'(?:gh[pousr]_[A-Za-z0-9]{30,}|github_pat_[A-Za-z0-9_]{30,}|AKIA[A-Z0-9]{16})',
+    rb'https?://[^\s/]+:[^\s/@]+@',
+]
+
+
+def require(value, message):
+    if not value:
+        raise ValueError(message)
+
+
+def sha(path):
+    digest = hashlib.sha256()
+    with path.open('rb') as stream:
+        for block in iter(lambda: stream.read(8 << 20), b''):
+            digest.update(block)
+    return digest.hexdigest()
+
+
+def ident(path):
+    return dict(bytes=path.stat().st_size, sha256=sha(path))
+
+
+def save(path, obj):
+    with path.open('x') as stream:
+        json.dump(obj, stream, indent=2, sort_keys=True, allow_nan=False)
+        stream.write('\n')
+
+
+def excluded(name):
+    if name.startswith(('cupy-cache-', 'brain-replay/build/')):
+        return 'Rebuildable compiler cache/SDK intermediates, not a scientific result'
+    if name in INSTALL_LOGS:
+        return 'Environment installation output; versions and wheel report retained'
+    return None
+
+
+def scan_text(path):
+    if path.suffix.lower() not in ('.json', '.jsonl', '.log', '.md', '.txt', '.csv', '.py', '.cu', '.diff'):
+        return
+    require(path.stat().st_size <= 25 * (1 << 20), 'Oversized text requires manual review')
+    data = path.read_bytes()
+    for rule in SECRET_RULES:
+        require(not re.search(rule, data), 'Potential credential marker: ' + path.name)
+
+
+def pack(root):
+    require(root == Path('/home/qishizhe/digital-drosophila-acceleration-publication-20261001'), 'Independent publication clone required')
+    require((root / '.git').is_dir() and not root.is_symlink(), 'Ordinary independent clone required')
+    registry, artifacts = root / REGISTRY, root / ARTIFACTS
+    registry.mkdir(parents=True, exist_ok=True)
+    artifacts.mkdir(parents=True, exist_ok=False)
+    catalog = dict(schema='acceleration-publication-v1', created_utc=datetime.now(timezone.utc).isoformat(),
+        numerical_changes=False, training_resumed=False, complete_training_restore=False,
+        scope='Two completed independent engineering experiments, not the full stopped scientific run', groups={})
+    for group, (source, expected_manifest, code_dir) in GROUPS.items():
+        require(sha(source / 'artifact-manifest.json') == expected_manifest, 'Sealed source manifest changed')
+        manifest = json.loads((source / 'artifact-manifest.json').read_text())
+        for name, expected in manifest['source_files'].items():
+            require(sha(SOURCE_CODE / code_dir / name) == expected, 'Sealed source code changed')
+            require(sha(root / 'models/male-cns-lif' / code_dir / name) == expected, 'Published source differs')
+        members, omitted = {}, {}
+        for name, expected in manifest['files'].items():
+            path = source / name
+            require(path.resolve().is_relative_to(source) and not path.is_symlink(), 'Unsafe source path')
+            require(ident(path) == expected, 'Sealed input file changed: ' + name)
+            reason = excluded(name)
+            if reason:
+                omitted[name] = dict(expected, reason=reason)
+            else:
+                scan_text(path)
+                members[group + '/' + name] = dict(expected, source_relative=name)
+        for name in ('artifact-manifest.json', 'SHA256SUMS'):
+            require(group + '/' + name not in members, 'Duplicate source control file')
+            members[group + '/' + name] = dict(ident(source / name), source_relative=name)
+        archive = artifacts / (group + '.tar.zst')
+        with archive.open('xb') as destination:
+            compressor = subprocess.Popen(['zstd', '-q', '-T2', '-3', '-c'], stdin=subprocess.PIPE, stdout=destination)
+            try:
+                with tarfile.open(fileobj=compressor.stdin, mode='w|', format=tarfile.PAX_FORMAT) as tar:
+                    for name, item in sorted(members.items()):
+                        path = source / item['source_relative']
+                        info = tarfile.TarInfo(name)
+                        info.size, info.mode, info.mtime = item['bytes'], 0o644, 0
+                        with path.open('rb') as stream:
+                            tar.addfile(info, stream)
+                        require(ident(path) == {k: item[k] for k in ('bytes', 'sha256')}, 'Input changed during packing')
+                compressor.stdin.close()
+                require(compressor.wait(timeout=120) == 0, 'Compression failed')
+            finally:
+                if compressor.poll() is None:
+                    compressor.kill()
+                    compressor.wait()
+        target = registry / group
+        target.mkdir(exist_ok=False)
+        for name in ('RESULTS.md', 'final-summary.json', 'artifact-manifest.json', 'SHA256SUMS'):
+            shutil.copyfile(source / name, target / name)
+            require(sha(source / name) == sha(target / name), 'Summary copy differs')
+        catalog['groups'][group] = dict(source_root=str(source), source_manifest_sha256=expected_manifest,
+            source_files=manifest['source_files'], archive=str(archive.relative_to(root)), **ident(archive),
+            member_count=len(members), member_bytes=sum(x['bytes'] for x in members.values()),
+            members=members, excluded=omitted, excluded_count=len(omitted))
+    save(registry / 'publication-catalog.json', catalog)
+    result = verify(root)
+    save(registry / 'pack-verification.json', result)
+    print(json.dumps(dict(complete=True, groups=result['groups'], source_files_modified=False), indent=2))
+
+
+def verify(root):
+    catalog_path = root / REGISTRY / 'publication-catalog.json'
+    catalog = json.loads(catalog_path.read_text())
+    require(catalog['schema'] == 'acceleration-publication-v1', 'Wrong publication catalog')
+    results = {}
+    for group, info in catalog['groups'].items():
+        archive = root / info['archive']
+        require(archive.resolve().is_relative_to(root / ARTIFACTS) and not archive.is_symlink(), 'Unsafe archive path')
+        require(ident(archive) == {k: info[k] for k in ('bytes', 'sha256')}, 'Archive identity mismatch')
+        decoder = subprocess.Popen(['zstd', '-q', '-d', '-c', str(archive)], stdout=subprocess.PIPE)
+        found, total = set(), 0
+        try:
+            with tarfile.open(fileobj=decoder.stdout, mode='r|') as tar:
+                for entry in tar:
+                    require(entry.isfile() and entry.name in info['members'] and entry.name not in found, 'Unexpected/duplicate member')
+                    expected = info['members'][entry.name]
+                    require(entry.size == expected['bytes'], 'Member size mismatch')
+                    h, count = hashlib.sha256(), 0
+                    with tar.extractfile(entry) as stream:
+                        for block in iter(lambda: stream.read(8 << 20), b''):
+                            h.update(block)
+                            count += len(block)
+                    require(count == entry.size and h.hexdigest() == expected['sha256'], 'Member hash mismatch')
+                    found.add(entry.name)
+                    total += count
+            while decoder.stdout.read(1 << 20):
+                pass
+            require(decoder.wait(timeout=30) == 0 and found == set(info['members']), 'Archive truncated or member set differs')
+        finally:
+            decoder.stdout.close()
+            if decoder.poll() is None:
+                decoder.kill()
+                decoder.wait()
+        results[group] = dict(files=len(found), original_bytes=total, archive_bytes=info['bytes'], sha256=info['sha256'], verified=True)
+    return dict(pass_all=True, groups=results, catalog_sha256=sha(catalog_path), verification='Full streamed members, no extraction or model execution')
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('mode', choices=('pack', 'verify'))
+    args = parser.parse_args()
+    if args.mode == 'pack':
+        pack(Path.cwd())
+    else:
+        print(json.dumps(verify(Path.cwd()), indent=2))
@@ -0,0 +1,68 @@
+"""Actual fresh-store remote retrieval; no scientific execution or retries."""
+import argparse
+from datetime import datetime, timezone
+import json
+from pathlib import Path
+import subprocess
+import time
+
+import archive_results as archives
+
+REMOTE = 'ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git'
+BRANCH = 'codex/v100-conditioning-acceleration'
+
+
+def cmd(args, output=False):
+    result = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    archives.require(result.returncode == 0, 'Git/LFS command failed; no automatic retry; diagnostic output not published')
+    return result.stdout.decode().strip() if output else result.returncode
+
+
+def run(expected, receipt):
+    root = Path.cwd()
+    archives.require(root == Path('/home/qishizhe/digital-drosophila-acceleration-verify-20261001')
+                     and (root / '.git').is_dir(), 'New independent verification clone required')
+    archives.require(cmd(['git', 'rev-parse', 'HEAD'], True) == expected, 'Unexpected checkout commit')
+    archives.require(cmd(['git', 'remote', 'get-url', 'origin'], True) == REMOTE, 'Unexpected remote')
+    remote_ref = cmd(['git', 'ls-remote', 'origin', 'refs/heads/' + BRANCH], True)
+    archives.require(remote_ref.split()[0] == expected, 'Remote branch does not identify data commit')
+    archives.require(not cmd(['git', 'status', '--porcelain'], True), 'Unclean initial checkout')
+    objects = root / '.git/lfs/objects'
+    before = list(p for p in objects.rglob('*') if p.is_file()) if objects.exists() else []
+    archives.require(not before, 'Fresh LFS object store must contain no prior object')
+    archives.require(not receipt.exists() and receipt.parent.is_dir()
+                     and receipt.parent == Path('/home/qishizhe/digital-drosophila-acceleration-publication-20261001/registry/acceleration-20261001'),
+                     'Exclusive publication receipt required')
+    start = time.perf_counter()
+    pull = cmd(['git', 'lfs', 'pull', '--include=artifacts/acceleration-20261001/**', '--exclude=', 'origin'])
+    fsck = cmd(['git', 'lfs', 'fsck', '--dry-run'])
+    report = archives.verify(root)
+    catalog = json.loads((root / archives.REGISTRY / 'publication-catalog.json').read_text())
+    source_count = 0
+    for group, info in catalog['groups'].items():
+        directory = archives.GROUPS[group][2]
+        for name, expected_sha in info['source_files'].items():
+            archives.require(archives.sha(root / 'models/male-cns-lif' / directory / name) == expected_sha,
+                             'Published source differs from sealed version')
+            source_count += 1
+    stored = [p for p in objects.rglob('*') if p.is_file()]
+    archives.require(len(stored) == 2 and not cmd(['git', 'status', '--porcelain'], True), 'Incomplete LFS store or changed checkout')
+    archives.require(cmd(['git', 'rev-parse', 'HEAD'], True) == expected, 'Checkout changed during verification')
+    report.update(schema='acceleration-fresh-remote-delivery-v1', verified_utc=datetime.now(timezone.utc).isoformat(),
+        remote=REMOTE, branch=BRANCH, data_commit=expected, fresh_download_proven=True,
+        initial_LFS_objects=0, downloaded_LFS_objects=len(stored), downloaded_bytes=sum(p.stat().st_size for p in stored),
+        pull_exit_code=pull, fsck_exit_code=fsck, sealed_source_files_checked=source_count,
+        wall_seconds=time.perf_counter()-start, scientific_experiments_run=0, training_resumed=False,
+        complete_training_restore=False, historical_scientific_gate_reexecuted=False,
+        transport='Previously audited LAN-pinned HTTPS adapter, verified TLS and SSH short-lived authorization',
+        scope='Remote Git commit, two actual LFS downloads, complete public archive contents and 22 sealed code files; not all external scientific dependencies')
+    archives.save(receipt, report)
+    print(json.dumps(report, indent=2))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--expected-commit', required=True)
+    parser.add_argument('--receipt', type=Path, required=True)
+    args = parser.parse_args()
+    run(args.expected_commit, args.receipt)
@@ -0,0 +1,336 @@
+"""Repository-local, LAN-pinned Git LFS standalone transfer agent.
+
+Protocol: https://github.com/git-lfs/git-lfs/blob/main/docs/custom-transfers.md
+Only fixed-origin SSH authentication and HTTPS basic transfers are supported.
+No config/network changes, retries, redirects, credential files, or cache-based
+download substitution. Credentials are passed to curl exclusively on stdin.
+"""
+from __future__ import annotations
+
+import hashlib
+import json
+import os
+from pathlib import Path
+import re
+import stat
+import subprocess
+import sys
+import tempfile
+from urllib.parse import urlsplit
+
+ORIGIN = "ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git"
+HOST = "git.lain.asia"
+IP = "192.168.10.31"
+PREFIX = "/qishizhe/digital-drosophila.git/info/lfs"
+SOURCE = Path("/data/digital-drosophila")
+OID = re.compile(r"^[0-9a-f]{64}$")
+HEADER = re.compile(r"^[!#$%&'*+.^_`|~0-9A-Za-z-]+$")
+MAX_JSON = 2 * 1024 * 1024
+BLOCK = 1024 * 1024
+
+
+class TransferError(Exception):
+    """Only fixed, non-secret messages may be passed to this class."""
+
+
+def require(ok, code):
+    if not ok:
+        raise TransferError(code)
+
+
+def decode_json(data):
+    def unique(pairs):
+        result = {}
+        for key, value in pairs:
+            require(key not in result, "duplicate-json-key")
+            result[key] = value
+        return result
+    require(len(data) <= MAX_JSON, "json-response-too-large")
+    try:
+        return json.loads(data, object_pairs_hook=unique)
+    except (UnicodeError, ValueError):
+        raise TransferError("invalid-json") from None
+
+
+def safe_path(value):
+    require(isinstance(value, (str, Path)), "invalid-file-path")
+    p = Path(value)
+    require(p.is_absolute() and ".." not in p.parts, "absolute-safe-path-required")
+    for component in (p, *p.parents):
+        if component.exists() or component.is_symlink():
+            s = component.lstat()
+            require(not stat.S_ISLNK(s.st_mode) and not
+                    (getattr(s, "st_file_attributes", 0) & getattr(stat, "FILE_ATTRIBUTE_REPARSE_POINT", 0)),
+                    "symlink-or-reparse-refused")
+    return p
+
+
+def safe_url(value):
+    require(isinstance(value, str) and len(value) <= 16384 and
+            not any(ord(c) <= 32 or ord(c) == 127 for c in value), "invalid-action-url")
+    try:
+        p = urlsplit(value)
+        valid = (p.scheme == "https" and p.netloc in (HOST, HOST + ":443") and
+                 p.hostname == HOST and p.port in (None, 443) and
+                 p.username is None and p.password is None and not p.fragment)
+    except ValueError:
+        raise TransferError("url-authority-refused") from None
+    require(valid, "url-authority-refused")
+    require(p.path == PREFIX or p.path.startswith(PREFIX + "/"), "url-repository-prefix-refused")
+    require("%" not in p.path and "\\" not in p.path and
+            all(x not in ("", ".", "..") for x in p.path.split("/")[1:]), "url-path-refused")
+    return value
+
+
+def safe_headers(value, *, allow_upload_chunked=False):
+    require(isinstance(value, dict) and len(value) <= 32, "invalid-action-headers")
+    result, seen = {}, set()
+    denied = {"host", "connection", "content-length", "transfer-encoding", "te",
+              "trailer", "upgrade", "proxy-authorization", "proxy-connection", "range"}
+    for key, item in value.items():
+        upload_chunked = (allow_upload_chunked is True and isinstance(key, str) and
+                          key.lower() == "transfer-encoding" and item == "chunked")
+        require(isinstance(key, str) and HEADER.fullmatch(key) is not None and
+                key.lower() not in seen and (key.lower() not in denied or upload_chunked),
+                "header-name-refused")
+        require(isinstance(item, str) and len(item) <= 16384 and
+                not any(ord(c) < 32 or ord(c) == 127 for c in item), "header-value-refused")
+        seen.add(key.lower())
+        result[key] = item
+    return result
+
+
+def quote(value):
+    require(isinstance(value, str) and not any(ord(c) < 32 or ord(c) == 127 for c in value),
+            "curl-config-value-refused")
+    return '"' + value.replace("\\", "\\\\").replace('"', '\\"') + '"'
+
+
+def fingerprint(s):
+    return (s.st_dev, s.st_ino, s.st_mode, s.st_size, s.st_mtime_ns, s.st_ctime_ns)
+
+
+def verify_file(path, oid, size):
+    path = safe_path(path)
+    before = fingerprint(path.lstat())
+    require(stat.S_ISREG(before[2]) and before[3] == size, "object-file-type-or-size-mismatch")
+    digest, count = hashlib.sha256(), 0
+    with path.open("rb") as handle:
+        opened = fingerprint(os.fstat(handle.fileno()))
+        # Windows path stat and fstat can expose different ctime definitions.
+        require(opened[:-1] == before[:-1] if os.name == "nt" else opened == before,
+                "object-changed-at-open")
+        while data := handle.read(BLOCK):
+            digest.update(data)
+            count += len(data)
+        require(fingerprint(os.fstat(handle.fileno())) == opened, "object-changed-during-read")
+    require(fingerprint(path.lstat()) == before and count == size and digest.hexdigest() == oid,
+            "object-sha-or-stability-mismatch")
+    return before
+
+
+def git_output(cwd, *args):
+    try:
+        result = subprocess.run(["git", "-C", str(cwd), *args], capture_output=True,
+                                timeout=15, check=False)
+        require(result.returncode == 0, "git-inspection-failed")
+        return result.stdout.decode("utf-8").strip()
+    except (OSError, UnicodeError, subprocess.TimeoutExpired):
+        raise TransferError("git-inspection-failed") from None
+
+
+class Agent:
+    def __init__(self, message, emit, cwd=None):
+        require(message.get("event") == "init" and message.get("operation") in ("upload", "download"),
+                "invalid-init")
+        require(message.get("remote") in ("origin", ORIGIN), "remote-refused")
+        concurrency = message.get("concurrenttransfers")
+        require(type(concurrency) is int and 1 <= concurrency <= 2 and
+                type(message.get("concurrent")) is bool, "concurrency-must-be-at-most-two")
+        cwd = safe_path(Path.cwd() if cwd is None else cwd)
+        require(cwd != SOURCE and SOURCE not in cwd.parents, "scientific-source-cwd-refused")
+        self.root = safe_path(git_output(cwd, "rev-parse", "--show-toplevel"))
+        require(self.root != SOURCE and SOURCE not in self.root.parents, "scientific-source-repository-refused")
+        require(git_output(cwd, "config", "--get", "remote.origin.url") == ORIGIN, "origin-refused")
+        self.git_dir = safe_path(git_output(cwd, "rev-parse", "--absolute-git-dir"))
+        require(self.git_dir == self.root / ".git" and self.git_dir.is_dir(), "ordinary-isolated-clone-required")
+        self.operation, self.emit = message["operation"], emit
+
+    def authenticate(self):
+        command = ["ssh", "-o", "BatchMode=yes", "-o", "StrictHostKeyChecking=yes",
+                   "-o", "ConnectTimeout=15", "-o", "ConnectionAttempts=1",
+                   "-o", "ServerAliveInterval=10", "-o", "ServerAliveCountMax=2",
+                   "-p", "2222", "git@192.168.10.31", "git-lfs-authenticate",
+                   "qishizhe/digital-drosophila.git", self.operation]
+        try:
+            result = subprocess.run(command, capture_output=True, timeout=45, check=False)
+            require(result.returncode == 0, "ssh-authentication-failed")
+            auth = decode_json(result.stdout)
+        except (OSError, subprocess.TimeoutExpired):
+            raise TransferError("ssh-authentication-failed") from None
+        require(isinstance(auth, dict), "invalid-ssh-authentication-response")
+        href = safe_url(auth.get("href"))
+        parsed = urlsplit(href)
+        require(parsed.path == PREFIX and not parsed.query, "authentication-base-url-refused")
+        return href, safe_headers(auth.get("header", {}))
+
+    def curl(self, method, url, headers, *, body=None, upload=None, download=None, size=None):
+        safe_url(url)
+        headers = safe_headers(headers, allow_upload_chunked=(self.operation == "upload" and
+                               method == "PUT" and upload is not None and body is None and download is None))
+        require(method in ("GET", "POST", "PUT"), "unsupported-http-method")
+        present = {name.lower() for name in headers}
+        if "accept" not in present:
+            headers["Accept"] = "application/vnd.git-lfs+json"
+        if method == "PUT" and "content-type" not in present:
+            headers["Content-Type"] = "application/octet-stream"
+        if body is not None and "content-type" not in present:
+            headers["Content-Type"] = "application/vnd.git-lfs+json"
+        lines = ["url = " + quote(url), "request = " + quote(method),
+                 'noproxy = "*"', 'resolve = "' + HOST + ':443:' + IP + '"',
+                 'proto = "=https"', 'proto-redir = "=https"', "max-redirs = 0",
+                 "connect-timeout = 15", "max-time = 1800", "fail", "silent", "show-error",
+                 'write-out = "\\n%{http_code}"']
+        for name, value in headers.items():
+            lines.append("header = " + quote(name + ": " + value))
+        if body is not None:
+            encoded = json.dumps(body, separators=(",", ":"), allow_nan=False)
+            lines.append("data-binary = " + quote(encoded))
+        if upload is not None:
+            lines.append("upload-file = " + quote(str(safe_path(upload))))
+        if download is not None:
+            lines.append("output = " + quote(str(safe_path(download))))
+            require(type(size) is int and size >= 0, "invalid-download-limit")
+            # A zero-byte object still needs a full HTTP fetch, not a cache hit.
+            lines.append("max-filesize = " + str(max(size, 1)))
+        else:
+            lines.append("max-filesize = " + str(MAX_JSON))
+        config = ("\n".join(lines) + "\n").encode("utf-8")
+        try:
+            result = subprocess.run(["curl", "-q", "--config", "-"], input=config,
+                                    capture_output=True, timeout=1830, check=False)
+        except (OSError, subprocess.TimeoutExpired):
+            raise TransferError("curl-execution-failed") from None
+        # Never print stderr, response data, URLs, configuration, or headers.
+        require(result.returncode == 0, "curl-request-failed")
+        require(len(result.stdout) <= MAX_JSON + 32, "http-response-too-large")
+        content, separator, status = result.stdout.rpartition(b"\n")
+        require(separator and len(status) == 3 and status.isdigit() and 200 <= int(status) < 300,
+                "non-success-http-status")
+        return content
+
+    def batch(self, oid, size):
+        href, headers = self.authenticate()
+        headers = {k: v for k, v in headers.items() if k.lower() not in ("content-type", "accept")}
+        headers.update({"Content-Type": "application/vnd.git-lfs+json", "Accept": "application/vnd.git-lfs+json"})
+        response = decode_json(self.curl("POST", href + "/objects/batch", headers,
+                                        body={"operation": self.operation, "transfers": ["basic"],
+                                              "objects": [{"oid": oid, "size": size}]}))
+        require(isinstance(response, dict) and response.get("transfer", "basic") == "basic",
+                "non-basic-batch-response")
+        objects = response.get("objects")
+        require(isinstance(objects, list) and len(objects) == 1 and isinstance(objects[0], dict),
+                "invalid-batch-object-count")
+        item = objects[0]
+        require(item.get("oid") == oid and type(item.get("size")) is int and item["size"] == size,
+                "batch-object-identity-mismatch")
+        require("error" not in item, "batch-object-rejected")
+        actions = item.get("actions", {})
+        require(isinstance(actions, dict), "invalid-batch-actions")
+        allowed = {"upload", "verify"} if self.operation == "upload" else {"download"}
+        require(set(actions) <= allowed, "unexpected-batch-action")
+        for name, action in actions.items():
+            require(isinstance(action, dict), "invalid-batch-action")
+            safe_url(action.get("href"))
+            safe_headers(action.get("header", {}), allow_upload_chunked=(self.operation == "upload" and name == "upload"))
+        return actions
+
+    def progress(self, oid, size, previous=0):
+        self.emit({"event": "progress", "oid": oid, "bytesSoFar": size, "bytesSinceLast": size - previous})
+
+    def transfer(self, message):
+        require(message.get("event") == self.operation and message.get("action") is None,
+                "standalone-operation-required")
+        oid, size = message.get("oid"), message.get("size")
+        require(isinstance(oid, str) and OID.fullmatch(oid) is not None and
+                type(size) is int and 0 <= size <= 2**63 - 1, "invalid-object-identity")
+        source, before = None, None
+        if self.operation == "upload":
+            source = safe_path(message.get("path"))
+            require(source == self.git_dir / "lfs" / "objects" / oid[:2] / oid[2:4] / oid,
+                    "upload-outside-current-lfs-object-store")
+            before = verify_file(source, oid, size)
+        actions = self.batch(oid, size)
+        self.progress(oid, 0)
+        if self.operation == "upload":
+            if "upload" in actions:
+                action = actions["upload"]
+                self.curl("PUT", action["href"], action.get("header", {}), upload=source)
+                require(fingerprint(source.lstat()) == before, "upload-source-changed")
+                if "verify" in actions:
+                    action = actions["verify"]
+                    headers = {k: v for k, v in action.get("header", {}).items() if k.lower() != "content-type"}
+                    headers["Content-Type"] = "application/vnd.git-lfs+json"
+                    self.curl("POST", action["href"], headers, body={"oid": oid, "size": size})
+            else:
+                require(not actions, "verify-without-upload-refused")
+                require(fingerprint(source.lstat()) == before, "upload-source-changed")
+            self.progress(oid, size)
+            return {"event": "complete", "oid": oid}
+        require("download" in actions, "download-action-missing")
+        directory = safe_path(self.git_dir / "lfs" / "lan-transfer-tmp")
+        directory.mkdir(parents=True, exist_ok=True)
+        safe_path(directory)
+        fd, name = tempfile.mkstemp(prefix=oid + ".", suffix=".partial", dir=directory)
+        os.close(fd)
+        target = Path(name)
+        action = actions["download"]
+        # On failure the uniquely created partial remains for investigation;
+        # it is never used as a fallback/cache input on a later transfer.
+        self.curl("GET", action["href"], action.get("header", {}), download=target, size=size)
+        verify_file(target, oid, size)
+        self.progress(oid, size)
+        return {"event": "complete", "oid": oid, "path": str(target)}
+
+
+def emit(value):
+    sys.stdout.write(json.dumps(value, separators=(",", ":"), allow_nan=False) + "\n")
+    sys.stdout.flush()
+
+
+def serve(inp=None, send=None, factory=Agent):
+    inp, send = sys.stdin if inp is None else inp, emit if send is None else send
+    agent = None
+    while True:
+        line = inp.readline(MAX_JSON + 1)
+        if not line:
+            return 0
+        try:
+            message = decode_json(line)
+            require(isinstance(message, dict), "protocol-object-required")
+            if agent is None:
+                agent = factory(message, send)
+                send({})
+            elif message.get("event") == "terminate":
+                return 0
+            else:
+                oid = message.get("oid")
+                safe_oid = oid if isinstance(oid, str) and OID.fullmatch(oid) else ""
+                try:
+                    send(agent.transfer(message))
+                except Exception as exc:
+                    code = str(exc) if isinstance(exc, TransferError) else "transfer-internal-failure"
+                    send({"event": "complete", "oid": safe_oid,
+                          "error": {"code": 2, "message": code}})
+        except Exception as exc:
+            code = str(exc) if isinstance(exc, TransferError) else "agent-initialization-or-protocol-failure"
+            if agent is None:
+                send({"error": {"code": 32, "message": code}})
+            else:
+                # No attacker-supplied raw line or exception text is printed.
+                sys.stderr.write("lan-lfs: invalid protocol; stopping\n")
+            return 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(serve())
@@ -0,0 +1,286 @@
+"""Pure temporary/mocked protocol tests: never SSH, curl, GPU, or real Git."""
+import contextlib
+import hashlib
+import io
+import json
+from pathlib import Path
+import subprocess
+import tempfile
+import unittest
+from unittest.mock import patch
+
+import lan_lfs_transfer as M
+
+BASE = "https://" + M.HOST + M.PREFIX
+TOKEN = "synthetic-fixture-" + "credential-value"
+
+
+class AdapterTests(unittest.TestCase):
+    def setUp(self):
+        self.temp = tempfile.TemporaryDirectory()
+        self.addCleanup(self.temp.cleanup)
+        self.root = Path(self.temp.name) / "clone"
+        self.git = self.root / ".git"
+        self.git.mkdir(parents=True)
+        self.data = b"synthetic content\x00\xff\n"
+        self.oid = hashlib.sha256(self.data).hexdigest()
+        self.size = len(self.data)
+        self.events = []
+        self.agent = object.__new__(M.Agent)
+        self.agent.root, self.agent.git_dir = self.root, self.git
+        self.agent.operation, self.agent.emit = "upload", self.events.append
+        self.source = self.git / "lfs" / "objects" / self.oid[:2] / self.oid[2:4] / self.oid
+        self.source.parent.mkdir(parents=True)
+        self.source.write_bytes(self.data)
+
+    def request(self, operation="upload", **extra):
+        value = {"event": operation, "oid": self.oid, "size": self.size, "action": None}
+        if operation == "upload":
+            value["path"] = str(self.source)
+        value.update(extra)
+        return value
+
+    def init_message(self, **extra):
+        return dict(event="init", operation="upload", remote="origin", concurrent=True,
+                    concurrenttransfers=2, **extra)
+
+    def action(self, suffix="objects/" ):
+        return {"href": BASE + "/" + suffix + self.oid,
+                "header": {"Authorization": "Bearer " + TOKEN}}
+
+    def test_strict_url_policy(self):
+        self.assertEqual(M.safe_url(BASE + "/objects/" + self.oid + "?signed=opaque"),
+                         BASE + "/objects/" + self.oid + "?signed=opaque")
+        invalid = [BASE.replace("https:", "http:"), BASE.replace(M.HOST, M.IP),
+                   BASE.replace(M.HOST, "other.example"), BASE.replace(M.HOST, M.HOST + ":444"),
+                   BASE.replace(M.HOST, "user:opaque@" + M.HOST), BASE + "-other/objects/x",
+                   BASE + "/../other", BASE + "/%2e%2e/other", BASE + "/objects/x#fragment",
+                   BASE + "//objects/x", BASE + "/objects\\x", BASE + "\n"]
+        for url in invalid:
+            with self.subTest(url=url), self.assertRaises(M.TransferError):
+                M.safe_url(url)
+
+    def test_headers_reject_injection_and_routing_overrides(self):
+        for headers in ({"Authorization": "x\r\nHost: bad"}, {"Host": "bad"},
+                        {"Authorization": "a", "authorization": "b"},
+                        {"Range": "bytes=1-"}, {"bad\nkey": "x"}, {"X": "\x00"}):
+            with self.subTest(headers=headers), self.assertRaises(M.TransferError):
+                M.safe_headers(headers)
+
+    def test_init_checks_origin_and_isolated_git_directory(self):
+        values = [str(self.root), M.ORIGIN, str(self.git)]
+        with patch.object(M, "git_output", side_effect=values):
+            actual = M.Agent(self.init_message(), self.events.append, cwd=self.root)
+        self.assertEqual(actual.git_dir, self.git)
+        with patch.object(M, "git_output", side_effect=[str(self.root), "ssh://other/repo"]):
+            with self.assertRaisesRegex(M.TransferError, "origin-refused"):
+                M.Agent(self.init_message(), self.events.append, cwd=self.root)
+
+    def test_original_source_and_excess_concurrency_refused(self):
+        with patch.object(M, "SOURCE", self.root):
+            with self.assertRaisesRegex(M.TransferError, "scientific-source-cwd"):
+                M.Agent(self.init_message(), self.events.append, cwd=self.root)
+        message = self.init_message()
+        message["concurrenttransfers"] = 3
+        with self.assertRaisesRegex(M.TransferError, "concurrency"):
+            M.Agent(message, self.events.append, cwd=self.root)
+
+    def test_ssh_authentication_is_strict_and_operation_scoped(self):
+        response = {"href": BASE, "header": {"Authorization": "Bearer " + TOKEN}}
+        result = subprocess.CompletedProcess([], 0, stdout=json.dumps(response).encode(), stderr=b"")
+        with patch.object(M.subprocess, "run", return_value=result) as call:
+            href, headers = self.agent.authenticate()
+        args = call.call_args.args[0]
+        self.assertIn("BatchMode=yes", args)
+        self.assertIn("StrictHostKeyChecking=yes", args)
+        self.assertEqual(args[-3:], ["git-lfs-authenticate", "qishizhe/digital-drosophila.git", "upload"])
+        self.assertEqual(href, BASE)
+        self.assertIn(TOKEN, headers["Authorization"])
+        self.assertNotIn(TOKEN, json.dumps(args))
+
+    def test_curl_secrets_only_in_stdin_and_secure_defaults(self):
+        result = subprocess.CompletedProcess([], 0, stdout=b"{}\n200", stderr=b"")
+        with patch.object(M.subprocess, "run", return_value=result) as call:
+            body = self.agent.curl("PUT", BASE + "/objects/" + self.oid + "?signature=" + TOKEN,
+                                   {"Authorization": "Bearer " + TOKEN}, upload=self.source)
+        self.assertEqual(body, b"{}")
+        self.assertEqual(call.call_args.args[0], ["curl", "-q", "--config", "-"])
+        self.assertNotIn(TOKEN, json.dumps(call.call_args.args[0]))
+        config = call.call_args.kwargs["input"].decode()
+        for wanted in ('noproxy = "*"', M.HOST + ":443:" + M.IP, 'proto = "=https"',
+                       "max-redirs = 0", "Accept: application/vnd.git-lfs+json",
+                       "Content-Type: application/octet-stream", TOKEN):
+            self.assertIn(wanted, config)
+        self.assertNotIn("insecure", config)
+        self.assertNotIn("location", config)
+        self.assertNotIn("retry", config)
+
+    def test_redirect_or_curl_error_is_sanitized(self):
+        for rc, output in ((0, b"redirect body\n302"), (22, b"")):
+            result = subprocess.CompletedProcess([], rc, stdout=output, stderr=TOKEN.encode())
+            with patch.object(M.subprocess, "run", return_value=result):
+                with self.assertRaises(M.TransferError) as caught:
+                    self.agent.curl("GET", BASE + "/objects/" + self.oid, {})
+            self.assertNotIn(TOKEN, str(caught.exception))
+
+    def test_post_json_sets_both_gitea_headers(self):
+        result = subprocess.CompletedProcess([], 0, stdout=b"\n204", stderr=b"")
+        with patch.object(M.subprocess, "run", return_value=result) as call:
+            self.agent.curl("POST", BASE + "/verify", {}, body={"oid": self.oid, "size": self.size})
+        config = call.call_args.kwargs["input"].decode()
+        self.assertIn("Accept: application/vnd.git-lfs+json", config)
+        self.assertIn("Content-Type: application/vnd.git-lfs+json", config)
+
+    def test_batch_requests_basic_and_checks_exact_identity(self):
+        response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": self.action()}}]}
+        with patch.object(self.agent, "authenticate", return_value=(BASE, {"Authorization": TOKEN})), \
+                patch.object(self.agent, "curl", return_value=json.dumps(response).encode()) as call:
+            self.assertIn("upload", self.agent.batch(self.oid, self.size))
+        args, kwargs = call.call_args
+        self.assertEqual(args[1], BASE + "/objects/batch")
+        self.assertEqual(args[2]["Accept"], "application/vnd.git-lfs+json")
+        self.assertEqual(kwargs["body"]["transfers"], ["basic"])
+        response["objects"][0]["size"] += 1
+        with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \
+                patch.object(self.agent, "curl", return_value=json.dumps(response).encode()):
+            with self.assertRaisesRegex(M.TransferError, "identity"):
+                self.agent.batch(self.oid, self.size)
+
+    def test_batch_action_host_rejected(self):
+        action = self.action()
+        action["href"] = action["href"].replace(M.HOST, "other.example")
+        response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": action}}]}
+        with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \
+                patch.object(self.agent, "curl", return_value=json.dumps(response).encode()):
+            with self.assertRaisesRegex(M.TransferError, "authority"):
+                self.agent.batch(self.oid, self.size)
+
+    def test_upload_chunked_exact_value_allowed_in_action_and_put(self):
+        action = self.action()
+        action["header"]["Transfer-Encoding"] = "chunked"
+        response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {"upload": action}}]}
+        with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \
+                patch.object(self.agent, "curl", return_value=json.dumps(response).encode()):
+            self.assertEqual(self.agent.batch(self.oid, self.size)["upload"]["header"]["Transfer-Encoding"], "chunked")
+        result = subprocess.CompletedProcess([], 0, stdout=b"\n200", stderr=b"")
+        with patch.object(M.subprocess, "run", return_value=result) as call:
+            self.agent.curl("PUT", action["href"], action["header"], upload=self.source)
+        config = call.call_args.kwargs["input"].decode()
+        self.assertIn('header = "Transfer-Encoding: chunked"', config)
+        self.assertIn('request = "PUT"', config)
+        self.assertIn("upload-file = ", config)
+
+    def test_chunked_forbidden_outside_upload_or_for_other_values(self):
+        for value in ("gzip", "CHUNKED", "chunked, gzip", "chunked\r\nX: y", " chunked"):
+            with self.subTest(value=value), self.assertRaises(M.TransferError):
+                self.agent.curl("PUT", BASE + "/objects/" + self.oid,
+                                {"Transfer-Encoding": value}, upload=self.source)
+        for method, kwargs in (("GET", {}), ("POST", {"body": {}}), ("PUT", {})):
+            with self.subTest(method=method, kwargs=kwargs), self.assertRaises(M.TransferError):
+                self.agent.curl(method, BASE + "/objects/" + self.oid,
+                                {"Transfer-Encoding": "chunked"}, **kwargs)
+        with self.assertRaises(M.TransferError):
+            M.safe_headers({"Transfer-Encoding": "chunked"})
+        for operation, name in (("upload", "verify"), ("download", "download")):
+            self.agent.operation = operation
+            action = self.action()
+            action["header"]["Transfer-Encoding"] = "chunked"
+            response = {"objects": [{"oid": self.oid, "size": self.size, "actions": {name: action}}]}
+            with patch.object(self.agent, "authenticate", return_value=(BASE, {})), \
+                    patch.object(self.agent, "curl", return_value=json.dumps(response).encode()):
+                with self.subTest(operation=operation, action=name), self.assertRaises(M.TransferError):
+                    self.agent.batch(self.oid, self.size)
+
+    def test_upload_existing_object_needs_no_put(self):
+        with patch.object(self.agent, "batch", return_value={}) as batch, patch.object(self.agent, "curl") as curl:
+            result = self.agent.transfer(self.request())
+        self.assertEqual(result, {"event": "complete", "oid": self.oid})
+        batch.assert_called_once()
+        curl.assert_not_called()
+        self.assertEqual(self.events[-1]["bytesSoFar"], self.size)
+
+    def test_upload_put_then_verification_post(self):
+        actions = {"upload": self.action(), "verify": self.action("verify/")}
+        with patch.object(self.agent, "batch", return_value=actions), \
+                patch.object(self.agent, "curl", return_value=b"") as curl:
+            self.agent.transfer(self.request())
+        self.assertEqual([c.args[0] for c in curl.call_args_list], ["PUT", "POST"])
+        self.assertEqual(curl.call_args_list[1].kwargs["body"], {"oid": self.oid, "size": self.size})
+
+    def test_upload_wrong_sha_fails_before_network(self):
+        self.source.write_bytes(b"x" * self.size)
+        with patch.object(self.agent, "batch") as batch:
+            with self.assertRaisesRegex(M.TransferError, "sha"):
+                self.agent.transfer(self.request())
+        batch.assert_not_called()
+
+    def test_upload_outside_lfs_store_refused(self):
+        other = self.root / self.oid
+        other.write_bytes(self.data)
+        with self.assertRaisesRegex(M.TransferError, "outside-current-lfs"):
+            self.agent.transfer(self.request(path=str(other)))
+
+    def test_upload_source_mutation_detected(self):
+        def change(*args, **kwargs):
+            self.source.write_bytes(b"changed")
+        with patch.object(self.agent, "batch", return_value={"upload": self.action()}), \
+                patch.object(self.agent, "curl", side_effect=change):
+            with self.assertRaisesRegex(M.TransferError, "upload-source-changed"):
+                self.agent.transfer(self.request())
+
+    def test_download_is_fresh_unique_and_verified(self):
+        self.agent.operation = "download"
+        def fetch(*args, **kwargs):
+            kwargs["download"].write_bytes(self.data)
+            return b""
+        with patch.object(self.agent, "batch", return_value={"download": self.action()}), \
+                patch.object(self.agent, "curl", side_effect=fetch) as curl:
+            first = self.agent.transfer(self.request("download"))
+            second = self.agent.transfer(self.request("download"))
+        self.assertNotEqual(first["path"], second["path"])
+        self.assertEqual(Path(first["path"]).read_bytes(), self.data)
+        self.assertEqual(curl.call_count, 2)
+        self.assertEqual(self.source.read_bytes(), self.data)
+
+    def test_download_hash_failure_retains_partial(self):
+        self.agent.operation = "download"
+        def fetch(*args, **kwargs):
+            kwargs["download"].write_bytes(b"x" * self.size)
+        with patch.object(self.agent, "batch", return_value={"download": self.action()}), \
+                patch.object(self.agent, "curl", side_effect=fetch):
+            with self.assertRaisesRegex(M.TransferError, "sha"):
+                self.agent.transfer(self.request("download"))
+        partials = list((self.git / "lfs" / "lan-transfer-tmp").glob("*.partial"))
+        self.assertEqual(len(partials), 1)
+        self.assertEqual(partials[0].read_bytes(), b"x" * self.size)
+
+    def test_protocol_init_progress_completion_terminate(self):
+        requests = [self.init_message(), self.request(), {"event": "terminate"}]
+        incoming = io.StringIO("".join(json.dumps(x) + "\n" for x in requests))
+        with patch.object(self.agent, "batch", return_value={}):
+            code = M.serve(incoming, self.events.append, factory=lambda message, send: self.agent)
+        self.assertEqual(code, 0)
+        self.assertEqual(self.events[0], {})
+        self.assertEqual(self.events[-1], {"event": "complete", "oid": self.oid})
+
+    def test_transfer_error_continues_and_never_echoes_exception_secret(self):
+        incoming = io.StringIO("\n".join(json.dumps(x) for x in
+                              [self.init_message(), self.request(), self.request(), {"event": "terminate"}]) + "\n")
+        with patch.object(self.agent, "transfer", side_effect=[RuntimeError(TOKEN), {"event": "complete", "oid": self.oid}]):
+            code = M.serve(incoming, self.events.append, factory=lambda message, send: self.agent)
+        self.assertEqual(code, 0)
+        self.assertIn("error", self.events[1])
+        self.assertNotIn(TOKEN, json.dumps(self.events))
+        self.assertNotIn("error", self.events[2])
+
+    def test_bad_initialization_uses_init_error_schema(self):
+        incoming = io.StringIO(json.dumps(self.init_message()) + "\n")
+        with patch.object(M, "git_output", side_effect=RuntimeError(TOKEN)):
+            code = M.serve(incoming, self.events.append)
+        self.assertEqual(code, 1)
+        self.assertEqual(self.events[0]["error"]["code"], 32)
+        self.assertNotIn(TOKEN, json.dumps(self.events))
+
+
+if __name__ == "__main__":
+    unittest.main()