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| Author | SHA1 | Date | |
|---|---|---|---|
| 27c4a93ca5 | |||
| 494b0f9c04 | |||
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| 5b1d1b72d7 | |||
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| 13cd0e0be7 | |||
| 7dc85baea9 | |||
| be41af186c |
@@ -1,4 +1,8 @@
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# Preserve historical source bytes and SHA-256 across platforms. No EOL conversion.
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# Preserve historical source bytes and SHA-256 across platforms. No EOL conversion.
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||||||
* -text
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* -text
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||||||
*.jsonl.gz binary
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*.jsonl.gz binary
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||||||
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artifacts/**/*.tar.zst filter=lfs diff=lfs merge=lfs -text
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artifacts/lfs-smoke/*.bin filter=lfs diff=lfs merge=lfs -text
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artifacts/public-resources-20261001/**/payload-*.bin filter=lfs diff=lfs merge=lfs -text
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artifacts/public-resources-20261001/**/*.jsonl.gz filter=lfs diff=lfs merge=lfs -text
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artifacts/acceleration-20261001/*.tar.zst filter=lfs diff=lfs merge=lfs -text
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artifacts/acceleration-20261001/*.tar.zst filter=lfs diff=lfs merge=lfs -text
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+2
-2
@@ -34,5 +34,5 @@ id_ed25519*
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|||||||
/registry/verification-runs/
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/registry/verification-runs/
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||||||
# Historical learned deltas/checkpoints are not source files.
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# Historical learned deltas/checkpoints are not source files.
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/models/learned/
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/models/learned/
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# Explicit, audited experiment exports only; original data stay ignored.
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# Explicit publication exports only; original scientific directories stay ignored.
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||||||
!/artifacts/acceleration-20261001/*.tar.zst
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!/artifacts/**/*.tar.zst
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+7
-1
@@ -1,6 +1,12 @@
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|||||||
# Digital Drosophila — 当前状态
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# Digital Drosophila — 当前状态
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||||||
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||||||
更新:2026-10-01。成果保存分支:`codex/v100-conditioning-acceleration`。
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更新:2026-10-01。统一成果入口:`main`。
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||||||
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||||||
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## 仓库整理(不是科学实验)
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||||||
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||||||
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CPU/GPU 加速成果与公开 LFS 资源按保留双亲的合并历史整合到 `main`。旧 7 个分支先按精确 SHA 创建 `archive/2026-10-01/*` 标签,再核验并清理远端分支;不改旧工作树、不修改已封存数据或模型。完整映射见[分支说明](docs/40-operations/branches-20261001.md),执行结果以 `registry/branch-consolidation-20261001/` 的实际回执为准。
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||||||
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||||||
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历史 registry 文档保留原字节,其旧分支恢复命令由[统一恢复指南](docs/30-reproducibility/main-restore.md)取代。
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## 最新状态:暂停研究,CPU/GPU 两套方案保留
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## 最新状态:暂停研究,CPU/GPU 两套方案保留
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||||||
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||||||
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@@ -2,6 +2,14 @@
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本仓库整理既有项目,不改变原始数据和软件的权属。尚未为本项目原创代码选定统一公开许可证;不得将“可访问此 Git 仓库”等同于取得任意再分发授权。
|
本仓库整理既有项目,不改变原始数据和软件的权属。尚未为本项目原创代码选定统一公开许可证;不得将“可访问此 Git 仓库”等同于取得任意再分发授权。
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## 2026-10-01 公开资源发布补充
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||||||
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用户已确认保留公开仓库,仅上传明确允许公开再分发的资源。[MaleCNS 官方下载页](https://male-cns.janelia.org/download/)已核实指向 [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)。据此,独立发布分支现在归档其已下载的数据及明确标注变更来源的既有派生数据;Cell Type Explorer、visualpathways、DoOR.data 和 Shiu 作者模型源码按各自原许可处理。作者署名、固定 commit、许可证据 SHA、排除项和恢复方法见 [本次发布说明](registry/publication-20261001/README.md)。FlyVis 不明确许可的资源、活动实验、环境和凭据不纳入。
|
||||||
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||||||
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下表保留初始化时的历史审查状态,不代表本次已核实许可仍然未知。新发布只在 `artifacts/` 增加只读快照,不覆盖原始数据或此前冻结索引;不为整个仓库补授统一许可证。
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## 初始化审查记录(2026-09-29)
|
||||||
|
|
||||||
| 外部资源 | 冻结副本中的许可证据 | 本仓库处理 |
|
| 外部资源 | 冻结副本中的许可证据 | 本仓库处理 |
|
||||||
|---|---|---|
|
|---|---|---|
|
||||||
| MaleCNS v1.0 官方数据 | 来源文件、原下载脚本和校验清单;统一再分发许可本次未确证 | 只登记路径、来源、大小、SHA-256;不上传数据 |
|
| MaleCNS v1.0 官方数据 | 来源文件、原下载脚本和校验清单;统一再分发许可本次未确证 | 只登记路径、来源、大小、SHA-256;不上传数据 |
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|||||||
@@ -1,11 +1,23 @@
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# Digital Drosophila / MaleCNS 全脑模型研究
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# Digital Drosophila / MaleCNS 全脑模型研究
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<!-- repository-metadata:start -->
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**中文简介**:围绕连接组、神经动力学与可塑性的数字果蝇研究。
|
||||||
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||||||
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**English summary**: Digital fruit-fly research covering connectomics, neural dynamics and plasticity.
|
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||||||
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| 中文标签 | English topic |
|
||||||
|
| --- | --- |
|
||||||
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| 研究 | `research` |
|
||||||
|
| 连接组 | `connectomics` |
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| 神经仿真 | `neural-simulation` |
|
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<!-- repository-metadata:end -->
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||||||
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。
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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。**
|
**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,最新正式封存科学阶段仍是 **Phase 4AQ:PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。
|
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。
|
**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)。
|
统一入口为 **`main`**,包含注册科学代码、CPU/GPU 两套方案及已公开的 LFS 数据。7 个旧分支的精确版本通过 `archive/2026-10-01/*` 标签保留,见[分支与恢复说明](docs/40-operations/branches-20261001.md)。这次只是仓库整理,不是生产运行时升级,也没有恢复训练。
|
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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。
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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`。
|
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。
|
`MaleCNS-TemporalEligibility-v2-candidate` 与 `MaleCNS-OlfactoryEncoder-v1-candidate` 保留。
|
||||||
@@ -21,7 +33,7 @@
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|||||||
| 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) |
|
| 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) |
|
||||||
| 模型边界 | [模型与冻结契约](docs/20-model/baseline.md) |
|
| 模型边界 | [模型与冻结契约](docs/20-model/baseline.md) |
|
||||||
| 论文、引用与证据用途 | [参考文献入口](references/README.md)、[证据边界](references/evidence-map.md) |
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| 论文、引用与证据用途 | [参考文献入口](references/README.md)、[证据边界](references/evidence-map.md) |
|
||||||
| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[恢复](docs/30-reproducibility/restore.md) |
|
| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[统一恢复入口](docs/30-reproducibility/main-restore.md) |
|
||||||
| Git 同步、大数据备份与安全 | [同步说明](docs/40-operations/git-sync.md)、[备份](docs/40-operations/backup.md) |
|
| Git 同步、大数据备份与安全 | [同步说明](docs/40-operations/git-sync.md)、[备份](docs/40-operations/backup.md) |
|
||||||
| 每个阶段的原始证据副本 | [阶段索引](registry/catalog-20260929/stages.json) |
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| 每个阶段的原始证据副本 | [阶段索引](registry/catalog-20260929/stages.json) |
|
||||||
| 全部科学文件路径/大小/SHA-256 | [快照说明](registry/README.md) |
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| 全部科学文件路径/大小/SHA-256 | [快照说明](registry/README.md) |
|
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@@ -38,17 +50,17 @@
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服务器项目根目录:`/data/digital-drosophila/`。
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服务器项目根目录:`/data/digital-drosophila/`。
|
||||||
远程:`ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git`。
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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`;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`。
|
统一主分支:`main`。历史版本由归档标签保留;原注册科学源码仍固定为 `80aeb2093db655329774eff7b32fb6e417b8b40b`,不随主分支移动。
|
||||||
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|
||||||
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。
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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。
|
||||||
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。
|
普通 Git 不直接保存大型科学二进制。**Git LFS** 保存获准公开再分发的原始/参考数据,以及本次 CPU/GPU 回放结果;两套原归档指针均原样整合到 `main`。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。
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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。
|
||||||
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。
|
只取得 Git pointer 不能恢复全数据;需按[统一恢复指南](docs/30-reproducibility/main-restore.md)下载所需 LFS 对象并验证内部成员。已封存报告中的旧分支命令仅作历史记录;不要据此重新运行实验。这不是全服务器灾备。
|
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## 安全的首次检查
|
## 安全的首次检查
|
||||||
|
|
||||||
```bash
|
```bash
|
||||||
GIT_LFS_SKIP_SMUDGE=1 git clone --branch codex/v100-conditioning-acceleration ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
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GIT_LFS_SKIP_SMUDGE=1 git clone --branch main ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
|
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cd digital-drosophila
|
cd digital-drosophila
|
||||||
python3 -B tools/repo_guard.py
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python3 -B tools/repo_guard.py
|
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```
|
```
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{
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"archive_bytes": 77971754,
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"archive_format": "tar.pax+zstd",
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"archive_sha256": "2366caef95fb5ad038639a6ae2ad25139a14c42492bc19640c20af46fefa0bc7",
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"chunk_bytes": 67108864,
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"chunks": [
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{
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"bytes": 67108864,
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"index": 0,
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"path": "payload-000000.bin",
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"sha256": "6f5830463b8a0077ae89e550ca45275d57cf7e81813c42bf66f89d13a42c03ee"
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},
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{
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"bytes": 10862890,
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"index": 1,
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"path": "payload-000001.bin",
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"sha256": "6b80b0133af06279bd30561f35042b679bd392b9236ee519d1e7ed9c4e85fb6a"
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}
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],
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"exclusion_records": 1,
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"exclusions": {
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"bytes": 144,
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"sha256": "c1bca109b61e53327fa7e01128a411d8ea328972593168c3ad6e1202dfdddc9c"
|
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|
},
|
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|
"group_id": "celltype-explorer",
|
||||||
|
"license": {
|
||||||
|
"evidence_file": "LICENSE",
|
||||||
|
"evidence_sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411",
|
||||||
|
"upstream": "CC-BY-4.0",
|
||||||
|
"url": "https://creativecommons.org/licenses/by/4.0/"
|
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|
},
|
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|
"members": {
|
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|
"bytes": 421593,
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"sha256": "8a51d3b4138bad12a520f8d1a12d54673416017d15fd1b1bcc49ed385da005bb"
|
||||||
|
},
|
||||||
|
"plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71",
|
||||||
|
"provenance": {
|
||||||
|
"attribution": "Reiser Lab and Male CNS Cell Type Explorer contributors; retain upstream notices",
|
||||||
|
"changes": "Unchanged pinned working-tree file bytes; .git, environments, caches and credentials excluded. A source snapshot, not a full Git clone.",
|
||||||
|
"commit": "789cc6c105798ce2fd70ba85dab394f90899616b",
|
||||||
|
"repository": "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns"
|
||||||
|
},
|
||||||
|
"schema": "lfs-publication-group-v1",
|
||||||
|
"secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules",
|
||||||
|
"source_bytes": 3957079583,
|
||||||
|
"source_files": 8973,
|
||||||
|
"source_paths": [
|
||||||
|
"experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer"
|
||||||
|
],
|
||||||
|
"source_root": "/data/digital-drosophila",
|
||||||
|
"verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
|
||||||
|
}
|
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{
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"archive_bytes": 901984,
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"archive_format": "tar.pax+zstd",
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"archive_sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1",
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"chunk_bytes": 67108864,
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"chunks": [
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{
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"bytes": 901984,
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|
"index": 0,
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"path": "payload-000000.bin",
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"sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1"
|
||||||
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}
|
||||||
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],
|
||||||
|
"exclusion_records": 1,
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||||||
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"exclusions": {
|
||||||
|
"bytes": 147,
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"sha256": "82627a482fd6adfc3abf4f83a30158fd8371b4532f425f7eb3b03044eb7e1367"
|
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|
},
|
||||||
|
"group_id": "door-data",
|
||||||
|
"license": {
|
||||||
|
"evidence_file": "DESCRIPTION",
|
||||||
|
"evidence_sha256": "27db2a92eb651d67969de94959990d51668a5857a33c4750a3b6ef49c5880504",
|
||||||
|
"upstream": "CC-BY-SA-4.0",
|
||||||
|
"url": "https://creativecommons.org/licenses/by-sa/4.0/"
|
||||||
|
},
|
||||||
|
"members": {
|
||||||
|
"bytes": 9486,
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||||||
|
"sha256": "ef13db49577b3b3d1c7c31aab117d911a2decc5a80ead66b6a350c43d16374b4"
|
||||||
|
},
|
||||||
|
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|
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|
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|
||||||
|
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|
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|
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|
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|
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|
||||||
|
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|
||||||
|
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|
||||||
|
"verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
|
||||||
|
}
|
||||||
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|
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|
"index": 68,
|
||||||
|
"path": "payload-000068.bin",
|
||||||
|
"sha256": "26222b3988412e52c10bd2a8cddd5b0a54409f16aa5e2367f9e6c3606760221d"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 69,
|
||||||
|
"path": "payload-000069.bin",
|
||||||
|
"sha256": "661e862287f8283794e812d5484dfc77651e6a9c44be2122f10b25e702dbf52d"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 70,
|
||||||
|
"path": "payload-000070.bin",
|
||||||
|
"sha256": "71de14c9a34cfed409f74d825c88a8b473cd509b1dd2619fe8d5a11da131bee0"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 71,
|
||||||
|
"path": "payload-000071.bin",
|
||||||
|
"sha256": "7c8b878109bae512ed7f411055d974e0669a31da88b561e87e4fbacbadb96375"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 72,
|
||||||
|
"path": "payload-000072.bin",
|
||||||
|
"sha256": "c75a839c07a242aa09dc0603b46cefd87ac79bfc6776dd4707f425f4afd143df"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 73,
|
||||||
|
"path": "payload-000073.bin",
|
||||||
|
"sha256": "af98e9729afc0d1406b7531e135ab4d932c34f9c38df81636026fdfe461fc400"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 67108864,
|
||||||
|
"index": 74,
|
||||||
|
"path": "payload-000074.bin",
|
||||||
|
"sha256": "8de906c2956b66594902536069870c6f4bfaa8221cae561a6f7a00ea9b3ab338"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"bytes": 30040253,
|
||||||
|
"index": 75,
|
||||||
|
"path": "payload-000075.bin",
|
||||||
|
"sha256": "98714008fee0cffd305c8e7b45d74d224033d013f7ea7a1759eb160ca0fff2f1"
|
||||||
|
}
|
||||||
|
],
|
||||||
|
"exclusion_records": 0,
|
||||||
|
"exclusions": {
|
||||||
|
"bytes": 20,
|
||||||
|
"sha256": "9ceffb7310338057cfe71a4ae1e2c98d2c485d81cdef906532a801f457a38d64"
|
||||||
|
},
|
||||||
|
"group_id": "malecns-synaptic-partners",
|
||||||
|
"license": {
|
||||||
|
"data": "CC-BY-4.0",
|
||||||
|
"local_provenance": "Project-authored",
|
||||||
|
"url": "https://creativecommons.org/licenses/by/4.0/"
|
||||||
|
},
|
||||||
|
"members": {
|
||||||
|
"bytes": 512,
|
||||||
|
"sha256": "cfe2adcc93576eeea4100b847016bd5484338f449d4755dc7071c4c621d4d6df"
|
||||||
|
},
|
||||||
|
"plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71",
|
||||||
|
"provenance": {
|
||||||
|
"attribution": "Male CNS collaboration: FlyEM (HHMI Janelia), University of Cambridge Department of Zoology, MRC Laboratory of Molecular Biology, Google Research",
|
||||||
|
"changes": "Unchanged downloaded paired-synapse file and provenance; syn-points and EM were not downloaded.",
|
||||||
|
"registered_file_sha256": "959d8ef4173b35382a3e6acfaf5167c795b6d10b877572d146af04e1b487bc07",
|
||||||
|
"source_page": "https://male-cns.janelia.org/download/",
|
||||||
|
"source_url": "https://storage.googleapis.com/flyem-male-cns/v1.0/connectome-data/flat-connectome/syn-partners-male-cns-v1.0-minconf-0.5.feather?generation=1780494942562468"
|
||||||
|
},
|
||||||
|
"schema": "lfs-publication-group-v1",
|
||||||
|
"secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules",
|
||||||
|
"source_bytes": 6777184219,
|
||||||
|
"source_files": 6,
|
||||||
|
"source_paths": [
|
||||||
|
"experiments/phase4aa-apl-pn-scope/external-resources"
|
||||||
|
],
|
||||||
|
"source_root": "/data/digital-drosophila",
|
||||||
|
"verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
|
||||||
|
}
|
||||||
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Reference in New Issue
Block a user