Add four checkpoints in a unified repository layout

.gitattributes

@@ -33,3 +33,31 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/activity-trace.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/eligibility.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/membrane.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/modulation.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/refractory.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/spikes.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/initial/checkpoint/weights.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/activity-trace.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/eligibility.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/membrane.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/modulation.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/refractory.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/spikes.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/canonical-v1/trained/checkpoint/weights.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/activity-trace.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/eligibility.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/membrane.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/modulation.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/refractory.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/spikes.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/after/checkpoint/weights.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/activity-trace.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/eligibility.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/membrane.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/modulation.f32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/refractory.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/spikes.u32le filter=lfs diff=lfs merge=lfs -text
+checkpoints/historical-video/before/checkpoint/weights.f32le filter=lfs diff=lfs merge=lfs -text

README.ja.md

@@ -4,14 +4,14 @@
 
 `virtual-fly`は、成体オスのショウジョウバエの公開MaleCNSコネクトームを初期状態として、神経活動・神経修飾・局所シナプス可塑性を時間発展させ、FlyBody / MuJoCoの身体と物理環境に閉ループ接続する研究プロジェクトです。
 
-このHugging Faceリポジトリでは、`virtual-fly`の概要と、初回公開に向けて準備しているチェックポイントリポジトリの構成をまとめています。ソースコード、科学的な説明、canonical実験のmanifest、一連の再現スクリプトはGitHubにあります。
+このHugging Faceリポジトリでは、`virtual-fly`の概要と、公開済みの4つのチェックポイントをまとめています。ソースコード、科学的な説明、canonical実験のmanifest、一連の再現スクリプトはGitHubにあります。
 
 - GitHub: https://github.com/shute2004/virtual-fly
 - 英語文書: https://github.com/shute2004/virtual-fly/tree/main/docs/en
 - 日本語README: https://github.com/shute2004/virtual-fly/blob/main/README.ja.md
 - 简体中文README: https://github.com/shute2004/virtual-fly/blob/main/README.zh-CN.md
 
-## チェックポイントの配布構成
+## チェックポイント
 
 公開チェックポイントには、明確に異なる2つの系統があります。**動画用のBefore / Afterをcanonical v1の初期・学習後チェックポイントとして扱わないでください。**
 
@@ -19,10 +19,10 @@
 
 canonical系の公開日は2026年9月20日です。
 
-| チェックポイント | リポジトリ | 意味 |
+| チェックポイント | ファイル | 意味 |
 |---|---|---|
-| 初期 | [`shute2004/virtual-fly-initial-20260920`](https://huggingface.co/shute2004/virtual-fly-initial-20260920) | canonical v1の初期チェックポイント。global weight version 0 |
-| 学習後 | [`shute2004/virtual-fly-trained-20260920`](https://huggingface.co/shute2004/virtual-fly-trained-20260920) | canonical v1で6エピソードの学習処理を経たチェックポイント。global weight version 6 |
+| 初期 | [`checkpoints/canonical-v1/initial`](checkpoints/canonical-v1/initial) | canonical v1の初期チェックポイント。global weight version 0 |
+| 学習後 | [`checkpoints/canonical-v1/trained`](checkpoints/canonical-v1/trained) | canonical v1で6エピソードの学習処理を経たチェックポイント。global weight version 6 |
 
 記録済みのcanonical v1実験は、実際にはGit commit `7fa464aad7269d34f46f1171080b51e095d1d811`で実行しました。公開前のprivacy-onlyな履歴書き換え後、公開用の科学コード相当commitは`f9c86c904d67ff974f3c43d37aab3619bc93fc1b`です。変更はhistorical absolute path内のローカルOSユーザー名だけで、実行コードやcanonical条件は変わっていません。この短いcanonical実験では、保存された25,582,938本の辺のうち2,163,179本で重みが変化しました。一方、可塑性とタスク由来のDAN刺激を無効化した固定評価では、初期・学習後とも同じ分類上の結果でした。
 
@@ -30,16 +30,16 @@ canonical系の公開日は2026年9月20日です。
 
 ### 過去系統のBefore / After動画
 
-| チェックポイント | リポジトリ | 来歴上の役割 |
+| チェックポイント | ファイル | 来歴上の役割 |
 |---|---|---|
-| Before | [`shute2004/virtual-fly-video-before`](https://huggingface.co/shute2004/virtual-fly-video-before) | 公開したBefore / After比較動画のBefore側で実際に使用した過去系統のチェックポイント |
-| After | [`shute2004/virtual-fly-video-after`](https://huggingface.co/shute2004/virtual-fly-video-after) | 同じ動画のAfter側で実際に使用した過去系統のチェックポイント |
+| Before | [`checkpoints/historical-video/before`](checkpoints/historical-video/before) | 公開したBefore / After比較動画のBefore側で実際に使用した過去系統のチェックポイント |
+| After | [`checkpoints/historical-video/after`](checkpoints/historical-video/after) | 同じ動画のAfter側で実際に使用した過去系統のチェックポイント |
 
 これらの内部開発版は来歴情報として`v240`と`v966`ですが、公開リポジトリ名には出しません。Before側のv240は未学習の初期状態ではなく、すでに240エピソードの過去学習を経ています。再生はホールドアウト評価ではなく、可塑性を停止した状態でも課題イベントによるPAM刺激は有効でした。v966も複数の過去条件が混在した系統です。したがって、これらは**canonical v1の証拠ではありません**。
 
 ## Hugging Faceに置くもの
 
-各チェックポイント用リポジトリには、チェックポイント本体と、必要最小限の来歴情報、ハッシュ値、帰属情報、モデルカードを置きます。研究用作業環境全体を複製するものではありません。
+各チェックポイントのディレクトリには、チェックポイント本体と、必要最小限の来歴情報、ハッシュ値、帰属情報、モデルカードを置きます。研究用作業環境全体を複製するものではありません。
 
 原則として置かないもの:
 
@@ -55,7 +55,7 @@ canonical系の公開日は2026年9月20日です。
 
 ## ライセンスと帰属
 
-`virtual-fly`独自のソースコードと文書はMIT Licenseで公開します。チェックポイントの重みは、MaleCNS公式サイトがCC BY 4.0で配布している`male-cns:v1.0`を基礎として生成した派生データです。そのため、チェックポイント用リポジトリは`cc-by-4.0`として明示し、MaleCNSへの帰属情報を付けます。
+`virtual-fly`独自のソースコードと文書はMIT Licenseで公開します。チェックポイントの重みは、MaleCNS公式サイトがCC BY 4.0で配布している`male-cns:v1.0`を基礎として生成した派生データです。そのため、チェックポイント成果物は`cc-by-4.0`として配布し、MaleCNSへの帰属情報を付けます。
 
 FlyBody、FlyGym、MuJoCoはそれぞれ上流のライセンスに従い、利便性だけを理由にチェックポイント用リポジトリへ複製しません。
 
@@ -72,4 +72,4 @@ uv sync --frozen
 bash canonical/canonical-v1/reproduce.sh
 ```
 
-Hugging Faceの各チェックポイントリポジトリは、チェックポイントを配布するためのものです。canonical v1の科学的な定義は、GitHub上のcanonicalパッケージを基準とします。
+Hugging Faceの各チェックポイントディレクトリは、チェックポイントを配布するためのものです。canonical v1の科学的な定義は、GitHub上のcanonicalパッケージを基準とします。

README.md

@@ -1,5 +1,5 @@
 ---
-license: mit
+license: cc-by-4.0
 language:
   - en
   - ja
@@ -20,14 +20,14 @@ tags:
 
 `virtual-fly` is a research project that starts from the released adult male Drosophila MaleCNS connectome and evolves neural activity, neuromodulation, and local synaptic plasticity in closed loop with a FlyBody / MuJoCo body and a physical environment.
 
-This Hugging Face repository provides an overview of `virtual-fly` and describes the checkpoint repositories published with the first public checkpoint release. Source code, scientific documentation, canonical manifests, and the end-to-end reproducer live on GitHub:
+This Hugging Face repository provides an overview of `virtual-fly` and hosts the four published checkpoints in one repository. Source code, scientific documentation, canonical manifests, and the end-to-end reproducer live on GitHub:
 
 - GitHub: https://github.com/shute2004/virtual-fly
 - English documentation: https://github.com/shute2004/virtual-fly/tree/main/docs/en
 - 日本語: https://github.com/shute2004/virtual-fly/blob/main/README.ja.md
 - 简体中文: https://github.com/shute2004/virtual-fly/blob/main/README.zh-CN.md
 
-## Checkpoint repositories
+## Checkpoints
 
 The checkpoint release has two distinct lineages. **Do not treat the historical video pair as the canonical initial/trained pair.**
 
@@ -35,25 +35,25 @@ The checkpoint release has two distinct lineages. **Do not treat the historical
 
 The canonical repository date is 2026-09-20.
 
-| Checkpoint | Repository | Meaning |
+| Checkpoint | Files | Meaning |
 |---|---|---|
-| Initial | [`shute2004/virtual-fly-initial-20260920`](https://huggingface.co/shute2004/virtual-fly-initial-20260920) | Initial checkpoint of canonical v1, global weight version 0 |
-| Trained | [`shute2004/virtual-fly-trained-20260920`](https://huggingface.co/shute2004/virtual-fly-trained-20260920) | Canonical v1 after six training episodes, global weight version 6 |
+| Initial | [`checkpoints/canonical-v1/initial`](checkpoints/canonical-v1/initial) | Initial checkpoint of canonical v1, global weight version 0 |
+| Trained | [`checkpoints/canonical-v1/trained`](checkpoints/canonical-v1/trained) | Canonical v1 after six training episodes, global weight version 6 |
 
 The recorded canonical v1 experiment was actually run at Git commit `7fa464aad7269d34f46f1171080b51e095d1d811`. Before public release, a privacy-only history rewrite produced public scientific equivalent `f9c86c904d67ff974f3c43d37aab3619bc93fc1b`; only historical absolute-path usernames changed, not executable source or canonical conditions. The short canonical run changed exactly 2,163,179 stored edges, but its frozen initial and final evaluations had the same categorical outcome. It therefore demonstrates current-semantics local-plasticity weight change, not established behavioral improvement.
 
 ### Historical Before / After video
 
-| Checkpoint | Repository | Provenance role |
+| Checkpoint | Files | Provenance role |
 |---|---|---|
-| Before | [`shute2004/virtual-fly-video-before`](https://huggingface.co/shute2004/virtual-fly-video-before) | Exact historical checkpoint used for the Before side of the published comparison video |
-| After | [`shute2004/virtual-fly-video-after`](https://huggingface.co/shute2004/virtual-fly-video-after) | Exact historical checkpoint used for the After side of the published comparison video |
+| Before | [`checkpoints/historical-video/before`](checkpoints/historical-video/before) | Exact historical checkpoint used for the Before side of the published comparison video |
+| After | [`checkpoints/historical-video/after`](checkpoints/historical-video/after) | Exact historical checkpoint used for the After side of the published comparison video |
 
 The historical cards record their internal development versions (`v240` and `v966`) as provenance, but those numbers are intentionally not used in the public repository names. The Before checkpoint is already a historically trained v240 state, not an untrained initial state; the playback was not held out and retained task-triggered PAM stimulation while plasticity was off. The v966 checkpoint belongs to a mixed older lineage. These checkpoints are **not canonical v1 evidence**.
 
 ## What is hosted here
 
-The checkpoint repositories contain checkpoint files plus lightweight provenance, hashes, attribution, and a model card. They do not mirror the full research workspace.
+Each checkpoint directory contains checkpoint files plus lightweight provenance, hashes, attribution, and a model card. They do not mirror the full research workspace.
 
 Not hosted here by default:
 
@@ -69,7 +69,7 @@ The official MaleCNS source and the GitHub canonical reproducer remain the acqui
 
 ## Licensing and attribution
 
-The original `virtual-fly` source code and documentation are MIT licensed. The checkpoint weights derive from the MaleCNS `male-cns:v1.0` dataset, which the official MaleCNS site distributes under CC BY 4.0. The checkpoint repositories are therefore marked `cc-by-4.0` and carry explicit MaleCNS attribution.
+The original `virtual-fly` source code and documentation are MIT licensed. The checkpoint weights derive from the MaleCNS `male-cns:v1.0` dataset, which the official MaleCNS site distributes under CC BY 4.0. The checkpoint artifacts are distributed under `cc-by-4.0` and carry explicit MaleCNS attribution.
 
 FlyBody, FlyGym, and MuJoCo remain under their upstream licenses and are not copied into the checkpoint repositories merely for convenience.
 
@@ -86,4 +86,4 @@ uv sync --frozen
 bash canonical/canonical-v1/reproduce.sh
 ```
 
-The Hugging Face checkpoint repositories are a distribution convenience. The GitHub canonical package remains the scientific definition of canonical v1.
+The Hugging Face checkpoint directories are a distribution convenience. The GitHub canonical package remains the scientific definition of canonical v1.

README.zh-CN.md

@@ -4,14 +4,14 @@
 
 `virtual-fly` 是一个研究项目：以成年雄性果蝇公开的 MaleCNS 连接组作为初始状态，让神经活动、神经调制和局部突触可塑性随时间演化，并与 FlyBody / MuJoCo 身体及物理环境形成闭环。
 
-这个 Hugging Face 仓库用于介绍 `virtual-fly`，并说明首次发布前已经准备好的检查点仓库结构。源代码、科学说明、canonical 实验清单以及完整复现脚本位于 GitHub：
+这个 Hugging Face 仓库用于介绍 `virtual-fly`，并在同一个仓库中提供四个已发布的检查点。源代码、科学说明、canonical 实验清单以及完整复现脚本位于 GitHub：
 
 - GitHub: https://github.com/shute2004/virtual-fly
 - 英文文档: https://github.com/shute2004/virtual-fly/tree/main/docs/en
 - 日本語 README: https://github.com/shute2004/virtual-fly/blob/main/README.ja.md
 - 简体中文 README: https://github.com/shute2004/virtual-fly/blob/main/README.zh-CN.md
 
-## 检查点仓库结构
+## 检查点
 
 公开检查点分为两个明确不同的系谱。**不要把视频用 Before / After 检查点当作 canonical v1 的初始 / 学习后检查点。**
 
@@ -19,10 +19,10 @@
 
 canonical 系列的发布日期为 2026 年 9 月 20 日。
 
-| 检查点 | 仓库 | 含义 |
+| 检查点 | 文件 | 含义 |
 |---|---|---|
-| 初始 | [`shute2004/virtual-fly-initial-20260920`](https://huggingface.co/shute2004/virtual-fly-initial-20260920) | canonical v1 的初始检查点，global weight version 0 |
-| 学习后 | [`shute2004/virtual-fly-trained-20260920`](https://huggingface.co/shute2004/virtual-fly-trained-20260920) | canonical v1 完成 6 个训练回合后的检查点，global weight version 6 |
+| 初始 | [`checkpoints/canonical-v1/initial`](checkpoints/canonical-v1/initial) | canonical v1 的初始检查点，global weight version 0 |
+| 学习后 | [`checkpoints/canonical-v1/trained`](checkpoints/canonical-v1/trained) | canonical v1 完成 6 个训练回合后的检查点，global weight version 6 |
 
 已记录的 canonical v1 实验实际运行于 Git commit `7fa464aad7269d34f46f1171080b51e095d1d811`。公开前只针对隐私进行历史重写后，公开使用的科学代码等价提交为 `f9c86c904d67ff974f3c43d37aab3619bc93fc1b`；变化仅限于历史绝对路径中的本地 OS 用户名，可执行源码和 canonical 条件均未改变。这次较短的 canonical 实验中，25,582,938 条存储边里有 2,163,179 条发生了权重变化。但在关闭可塑性和任务触发 DAN 刺激的固定评估中，初始状态和学习后状态的分类结果相同。
 
@@ -30,16 +30,16 @@ canonical 系列的发布日期为 2026 年 9 月 20 日。
 
 ### 历史 Before / After 视频
 
-| 检查点 | 仓库 | 来源角色 |
+| 检查点 | 文件 | 来源角色 |
 |---|---|---|
-| Before | [`shute2004/virtual-fly-video-before`](https://huggingface.co/shute2004/virtual-fly-video-before) | 公开 Before / After 对比视频中 Before 一侧实际使用的历史检查点 |
-| After | [`shute2004/virtual-fly-video-after`](https://huggingface.co/shute2004/virtual-fly-video-after) | 同一视频中 After 一侧实际使用的历史检查点 |
+| Before | [`checkpoints/historical-video/before`](checkpoints/historical-video/before) | 公开 Before / After 对比视频中 Before 一侧实际使用的历史检查点 |
+| After | [`checkpoints/historical-video/after`](checkpoints/historical-video/after) | 同一视频中 After 一侧实际使用的历史检查点 |
 
 这些检查点的内部开发版本分别是 `v240` 和 `v966`，但这些编号不会出现在公开仓库名中，只保留在来源记录里。Before 一侧的 v240 不是未经学习的初始状态，而是已经经历 240 个历史训练回合的检查点；回放不是留出评估，而且在关闭可塑性时仍保留了任务事件触发的 PAM 刺激。v966 也来自混合了多个早期条件的开发系。因此，它们**不是 canonical v1 的实验依据**。
 
 ## Hugging Face 中保存什么
 
-正式发布后，每个检查点仓库只保存检查点本体，以及直接需要的来源记录、哈希值、归属信息和模型卡。它们不会复制整个研究工作区。
+正式发布后，每个检查点目录只保存检查点本体，以及直接需要的来源记录、哈希值、归属信息和模型卡。它们不会复制整个研究工作区。
 
 默认不保存：
 
@@ -55,7 +55,7 @@ canonical 系列的发布日期为 2026 年 9 月 20 日。
 
 ## 许可证与归属
 
-`virtual-fly` 原创源代码和文档使用 MIT License。检查点权重以 MaleCNS 官方站点按 CC BY 4.0 发布的 `male-cns:v1.0` 为基础，因此检查点仓库标记为 `cc-by-4.0`，并明确保留 MaleCNS 归属信息。
+`virtual-fly` 原创源代码和文档使用 MIT License。检查点权重以 MaleCNS 官方站点按 CC BY 4.0 发布的 `male-cns:v1.0` 为基础，因此检查点成果物按 `cc-by-4.0` 分发，并明确保留 MaleCNS 归属信息。
 
 FlyBody、FlyGym 和 MuJoCo 继续适用各自的上游许可证，不会仅为方便而复制进检查点仓库。
 
@@ -72,4 +72,4 @@ uv sync --frozen
 bash canonical/canonical-v1/reproduce.sh
 ```
 
-Hugging Face 上的各检查点仓库用于分发检查点文件。canonical v1 的科学定义仍以 GitHub 中的 canonical 包为准。
+Hugging Face 上的各检查点目录用于分发检查点文件。canonical v1 的科学定义仍以 GitHub 中的 canonical 包为准。

checkpoints/README.md

@@ -0,0 +1,12 @@
+# Checkpoints
+
+Four checkpoints are provided in two deliberately separate lineages.
+
+| Lineage | Checkpoint | Path |
+|---|---|---|
+| Canonical v1 | Initial | [`canonical-v1/initial`](canonical-v1/initial) |
+| Canonical v1 | Trained (6 episodes) | [`canonical-v1/trained`](canonical-v1/trained) |
+| Historical video | Before | [`historical-video/before`](historical-video/before) |
+| Historical video | After | [`historical-video/after`](historical-video/after) |
+
+The historical Before/After pair is **not** the canonical initial/trained pair. Each directory contains provenance, SHA-256 hashes, attribution, and the native checkpoint files.

checkpoints/canonical-v1/initial/ATTRIBUTION.md

@@ -0,0 +1,14 @@
+# Attribution and license
+
+The checkpoint weights in this checkpoint directory derive from the released MaleCNS `male-cns:v1.0` connectome. The official MaleCNS download page distributes that dataset under **Creative Commons Attribution 4.0 International (CC BY 4.0)**.
+
+- MaleCNS project: https://male-cns.janelia.org/
+- Official download: https://male-cns.janelia.org/download/
+- License: https://creativecommons.org/licenses/by/4.0/
+- Primary MaleCNS reference: Bates et al. (2026), *Distributed control circuits across a brain-and-cord connectome*, Nature.
+
+`virtual-fly` transforms the upstream connectome into a simulation checkpoint and, for trained/historical states, may contain subsequent locally computed synaptic-weight changes. This checkpoint artifact is therefore distributed as CC BY 4.0 and identifies it as a derived numerical state.
+
+Original `virtual-fly` source code and documentation are MIT licensed. No raw MaleCNS download, FlyBody asset, FlyGym source, or MuJoCo source is redistributed in this Hugging Face repository. Those upstream resources remain under their own licenses and should be obtained from their official projects.
+
+Detailed third-party notices: https://github.com/shute2004/virtual-fly/blob/main/THIRD_PARTY_NOTICES.md

checkpoints/canonical-v1/initial/README.md

@@ -0,0 +1,67 @@
+---
+license: cc-by-4.0
+language:
+  - en
+tags:
+  - drosophila
+  - connectome
+  - computational-neuroscience
+  - neuromodulation
+  - synaptic-plasticity
+  - virtual-fly
+  - checkpoint
+  - reproducible-research
+---
+
+# virtual-fly canonical initial checkpoint
+
+> **Lineage:** Canonical v1 initial state
+
+This is the initial checkpoint of the current `virtual-fly` canonical experiment. **Initial does not mean a randomly initialized artificial neural network.** It means the initial neural checkpoint used by canonical v1 after constructing the simulation state from the released MaleCNS connectome and the canonical runtime assumptions.
+
+This checkpoint was produced by the recorded canonical v1 experiment at original Git commit `7fa464aad7269d34f46f1171080b51e095d1d811`. Its privacy-redacted public scientific equivalent is `f9c86c904d67ff974f3c43d37aab3619bc93fc1b`; the rewrite changed only historical local-path usernames, not executable source or canonical conditions. This checkpoint is global weight version **0** at aggregate neural step **0**.
+
+## Checkpoint semantics
+
+The manifest declares `checkpoint_semantics=global-weights-only-v1` and `step_semantics=aggregate-slot-neural-step-count-v1`. The on-disk layout contains the full set of checkpoint arrays for loader compatibility, but canonical population training persists only the **global synaptic weights** across episodes. Membrane, spike, refractory, activity-trace, modulation, eligibility, body, and peripheral state are reset between episodes. Do not interpret the directory as a continuously persistent whole-fly biological state.
+
+## Relationship to the trained checkpoint
+
+The corresponding canonical trained checkpoint will be published as [`../trained`](../trained) using the same actual publication date. The short canonical run changed exactly **2,163,179** stored edges. Its frozen initial and final evaluations had the same categorical outcome, so the pair demonstrates current-semantics weight change rather than established behavioral improvement.
+
+## Source code and reproducibility
+
+- Project overview: https://huggingface.co/shute2004/virtual-fly
+- GitHub source: https://github.com/shute2004/virtual-fly
+- Canonical package: https://github.com/shute2004/virtual-fly/tree/main/canonical/canonical-v1
+- Full artifact hash manifest: https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json
+
+The checkpoint is not self-contained without a compatible MaleCNS snapshot and the `virtual-fly` runtime. Raw MaleCNS is intentionally not mirrored here; obtain it from the official MaleCNS source or use the GitHub reproduction path.
+
+## Directory contents
+
+```text
+README.md
+ATTRIBUTION.md
+provenance.json
+SHA256SUMS
+checkpoint/
+  manifest.json
+  membrane.f32le
+  spikes.u32le
+  refractory.u32le
+  activity-trace.f32le
+  modulation.f32le
+  weights.f32le
+  eligibility.f32le
+```
+
+The checkpoint directory is kept in the native `virtual-fly` checkpoint layout so that the source repository can consume it without repacking. Raw MaleCNS source data and body assets are intentionally not included.
+
+## Integrity
+
+`SHA256SUMS` records the exact hashes of the original checkpoint files selected for publication. Verify the checkpoint before use.
+
+## License and upstream attribution
+
+The checkpoint artifact is distributed as **CC BY 4.0** because its weights derive from the CC BY 4.0 MaleCNS dataset. See `ATTRIBUTION.md`. Original `virtual-fly` source code and documentation remain MIT licensed.

checkpoints/canonical-v1/initial/SHA256SUMS

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+59bc68b376b730245aa0a6187794bf1b8bb5cf893925f731adc6d454c4034d10  checkpoint/modulation.f32le
+59bc68b376b730245aa0a6187794bf1b8bb5cf893925f731adc6d454c4034d10  checkpoint/refractory.u32le
+59bc68b376b730245aa0a6187794bf1b8bb5cf893925f731adc6d454c4034d10  checkpoint/spikes.u32le
+4b158ecce6c851c9a321a5e64cafcc75362e398a485a080494771c1dc3e019ce  checkpoint/weights.f32le

checkpoints/canonical-v1/initial/checkpoint/activity-trace.f32le

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+size 666800

checkpoints/canonical-v1/initial/checkpoint/eligibility.f32le

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checkpoints/canonical-v1/initial/checkpoint/manifest.json

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+{
+  "schema_version": 3,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "step": 0,
+  "global_weight_version": 0,
+  "checkpoint_semantics": "global-weights-only-v1",
+  "step_semantics": "aggregate-slot-neural-step-count-v1",
+  "membrane_file": "membrane.f32le",
+  "spikes_file": "spikes.u32le",
+  "refractory_file": "refractory.u32le",
+  "activity_trace_file": "activity-trace.f32le",
+  "modulation_file": "modulation.f32le",
+  "weights_file": "weights.f32le",
+  "eligibility_file": "eligibility.f32le"
+}

checkpoints/canonical-v1/initial/checkpoint/membrane.f32le

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+size 666800

checkpoints/canonical-v1/initial/checkpoint/modulation.f32le

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+oid sha256:59bc68b376b730245aa0a6187794bf1b8bb5cf893925f731adc6d454c4034d10
+size 666800

checkpoints/canonical-v1/initial/checkpoint/refractory.u32le

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+size 666800

checkpoints/canonical-v1/initial/checkpoint/spikes.u32le

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checkpoints/canonical-v1/initial/checkpoint/weights.f32le

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+size 102331752

checkpoints/canonical-v1/initial/provenance.json

@@ -0,0 +1,21 @@
+{
+  "schema_version": 1,
+  "artifact_id": "canonical-initial",
+  "lineage": "canonical-v1",
+  "historical": false,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "global_weight_version": 0,
+  "source_locator": "external-reference:canonical-v1-reference/artifacts/canonical-experiment-v1/initial/checkpoint",
+  "source_hash_manifest": "https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json",
+  "malecns_official_source": "https://male-cns.janelia.org/download/",
+  "malecns_license": "CC-BY-4.0",
+  "original_experiment_git_sha": "7fa464aad7269d34f46f1171080b51e095d1d811",
+  "public_equivalent_git_sha": "f9c86c904d67ff974f3c43d37aab3619bc93fc1b",
+  "aggregate_neural_step": 0,
+  "checkpoint_semantics": "global-weights-only-v1",
+  "step_semantics": "aggregate-slot-neural-step-count-v1",
+  "repository": "shute2004/virtual-fly",
+  "path": "checkpoints/canonical-v1/initial"
+}

checkpoints/canonical-v1/trained/ATTRIBUTION.md

@@ -0,0 +1,14 @@
+# Attribution and license
+
+The checkpoint weights in this checkpoint directory derive from the released MaleCNS `male-cns:v1.0` connectome. The official MaleCNS download page distributes that dataset under **Creative Commons Attribution 4.0 International (CC BY 4.0)**.
+
+- MaleCNS project: https://male-cns.janelia.org/
+- Official download: https://male-cns.janelia.org/download/
+- License: https://creativecommons.org/licenses/by/4.0/
+- Primary MaleCNS reference: Bates et al. (2026), *Distributed control circuits across a brain-and-cord connectome*, Nature.
+
+`virtual-fly` transforms the upstream connectome into a simulation checkpoint and, for trained/historical states, may contain subsequent locally computed synaptic-weight changes. This checkpoint artifact is therefore distributed as CC BY 4.0 and identifies it as a derived numerical state.
+
+Original `virtual-fly` source code and documentation are MIT licensed. No raw MaleCNS download, FlyBody asset, FlyGym source, or MuJoCo source is redistributed in this Hugging Face repository. Those upstream resources remain under their own licenses and should be obtained from their official projects.
+
+Detailed third-party notices: https://github.com/shute2004/virtual-fly/blob/main/THIRD_PARTY_NOTICES.md

checkpoints/canonical-v1/trained/README.md

@@ -0,0 +1,67 @@
+---
+license: cc-by-4.0
+language:
+  - en
+tags:
+  - drosophila
+  - connectome
+  - computational-neuroscience
+  - neuromodulation
+  - synaptic-plasticity
+  - virtual-fly
+  - checkpoint
+  - reproducible-research
+---
+
+# virtual-fly canonical trained checkpoint
+
+> **Lineage:** Canonical v1 post-training state
+
+This is the checkpoint produced after the six training episodes of the current `virtual-fly` canonical experiment. It is part of the same canonical lineage as [`../initial`](../initial), not the historical Before/After video lineage.
+
+This checkpoint was produced by the recorded canonical v1 experiment at original Git commit `7fa464aad7269d34f46f1171080b51e095d1d811`. Its privacy-redacted public scientific equivalent is `f9c86c904d67ff974f3c43d37aab3619bc93fc1b`; the rewrite changed only historical local-path usernames, not executable source or canonical conditions. This checkpoint is global weight version **6** at aggregate neural step **484**. Exactly **2,163,179 / 25,582,938** stored edges differ from the canonical initial checkpoint.
+
+## Checkpoint semantics
+
+The manifest declares `checkpoint_semantics=global-weights-only-v1` and `step_semantics=aggregate-slot-neural-step-count-v1`. The checkpoint is serialized in the full native file layout for loader compatibility, but only global weights are persistent population state. Other neural-dynamic and embodied state is reset between episodes.
+
+## Result boundary
+
+Frozen evaluation disables both plasticity and task-triggered DAN stimulation. The recorded canonical initial and final evaluations both passed one gate and then collided at control step 120. Therefore this checkpoint is evidence of local-plasticity-driven stored-weight change under current semantics, **not** a claim that canonical v1 established categorical behavioral improvement, generalization, or long-term learning stability.
+
+## Source code and reproducibility
+
+- Project overview: https://huggingface.co/shute2004/virtual-fly
+- GitHub source: https://github.com/shute2004/virtual-fly
+- Canonical package: https://github.com/shute2004/virtual-fly/tree/main/canonical/canonical-v1
+- Full artifact hash manifest: https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json
+
+The checkpoint is not self-contained without a compatible MaleCNS snapshot and the `virtual-fly` runtime. Raw MaleCNS is intentionally not mirrored here; obtain it from the official MaleCNS source or use the GitHub reproduction path.
+
+## Directory contents
+
+```text
+README.md
+ATTRIBUTION.md
+provenance.json
+SHA256SUMS
+checkpoint/
+  manifest.json
+  membrane.f32le
+  spikes.u32le
+  refractory.u32le
+  activity-trace.f32le
+  modulation.f32le
+  weights.f32le
+  eligibility.f32le
+```
+
+The checkpoint directory is kept in the native `virtual-fly` checkpoint layout so that the source repository can consume it without repacking. Raw MaleCNS source data and body assets are intentionally not included.
+
+## Integrity
+
+`SHA256SUMS` records the exact hashes of the original checkpoint files selected for publication. Verify the checkpoint before use.
+
+## License and upstream attribution
+
+The checkpoint artifact is distributed as **CC BY 4.0** because its weights derive from the CC BY 4.0 MaleCNS dataset. See `ATTRIBUTION.md`. Original `virtual-fly` source code and documentation remain MIT licensed.

checkpoints/canonical-v1/trained/SHA256SUMS

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+59bc68b376b730245aa0a6187794bf1b8bb5cf893925f731adc6d454c4034d10  checkpoint/spikes.u32le
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+size 666800

checkpoints/canonical-v1/trained/checkpoint/eligibility.f32le

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checkpoints/canonical-v1/trained/checkpoint/manifest.json

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+{
+  "schema_version": 3,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "step": 484,
+  "global_weight_version": 6,
+  "checkpoint_semantics": "global-weights-only-v1",
+  "step_semantics": "aggregate-slot-neural-step-count-v1",
+  "membrane_file": "membrane.f32le",
+  "spikes_file": "spikes.u32le",
+  "refractory_file": "refractory.u32le",
+  "activity_trace_file": "activity-trace.f32le",
+  "modulation_file": "modulation.f32le",
+  "weights_file": "weights.f32le",
+  "eligibility_file": "eligibility.f32le"
+}

checkpoints/canonical-v1/trained/checkpoint/membrane.f32le

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checkpoints/canonical-v1/trained/checkpoint/modulation.f32le

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checkpoints/canonical-v1/trained/checkpoint/refractory.u32le

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checkpoints/canonical-v1/trained/checkpoint/spikes.u32le

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checkpoints/canonical-v1/trained/checkpoint/weights.f32le

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checkpoints/canonical-v1/trained/provenance.json

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+{
+  "schema_version": 1,
+  "artifact_id": "canonical-trained",
+  "lineage": "canonical-v1",
+  "historical": false,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "global_weight_version": 6,
+  "source_locator": "external-reference:canonical-v1-reference/artifacts/canonical-experiment-v1/training/checkpoint",
+  "source_hash_manifest": "https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json",
+  "malecns_official_source": "https://male-cns.janelia.org/download/",
+  "malecns_license": "CC-BY-4.0",
+  "original_experiment_git_sha": "7fa464aad7269d34f46f1171080b51e095d1d811",
+  "public_equivalent_git_sha": "f9c86c904d67ff974f3c43d37aab3619bc93fc1b",
+  "aggregate_neural_step": 484,
+  "checkpoint_semantics": "global-weights-only-v1",
+  "step_semantics": "aggregate-slot-neural-step-count-v1",
+  "changed_edges_from_canonical_initial": 2163179,
+  "repository": "shute2004/virtual-fly",
+  "path": "checkpoints/canonical-v1/trained"
+}

checkpoints/historical-video/after/ATTRIBUTION.md

@@ -0,0 +1,14 @@
+# Attribution and license
+
+The checkpoint weights in this checkpoint directory derive from the released MaleCNS `male-cns:v1.0` connectome. The official MaleCNS download page distributes that dataset under **Creative Commons Attribution 4.0 International (CC BY 4.0)**.
+
+- MaleCNS project: https://male-cns.janelia.org/
+- Official download: https://male-cns.janelia.org/download/
+- License: https://creativecommons.org/licenses/by/4.0/
+- Primary MaleCNS reference: Bates et al. (2026), *Distributed control circuits across a brain-and-cord connectome*, Nature.
+
+`virtual-fly` transforms the upstream connectome into a simulation checkpoint and, for trained/historical states, may contain subsequent locally computed synaptic-weight changes. This checkpoint artifact is therefore distributed as CC BY 4.0 and identifies it as a derived numerical state.
+
+Original `virtual-fly` source code and documentation are MIT licensed. No raw MaleCNS download, FlyBody asset, FlyGym source, or MuJoCo source is redistributed in this Hugging Face repository. Those upstream resources remain under their own licenses and should be obtained from their official projects.
+
+Detailed third-party notices: https://github.com/shute2004/virtual-fly/blob/main/THIRD_PARTY_NOTICES.md

checkpoints/historical-video/after/README.md

@@ -0,0 +1,71 @@
+---
+license: cc-by-4.0
+language:
+  - en
+tags:
+  - drosophila
+  - connectome
+  - computational-neuroscience
+  - neuromodulation
+  - synaptic-plasticity
+  - virtual-fly
+  - checkpoint
+  - reproducible-research
+---
+
+# virtual-fly historical video After checkpoint
+
+> **Lineage:** Historical After-video state
+
+This directory contains the exact historical checkpoint used for the **After** side of the published `virtual-fly` Before/After comparison video. It is intentionally separated from the current canonical trained checkpoint.
+
+Internal provenance: global weight version **966**, checkpoint neural step **164,754**, source experiment `flyppy-v7h-online-video-v966`. The public repository name deliberately omits `v966`; the version is retained here only as historical provenance.
+
+## Historical semantics
+
+This checkpoint predates the explicit current population-checkpoint contract: its original manifest does **not** declare `global-weights-only-v1` or current class-DAN provenance. It must not be silently relabeled as a canonical checkpoint. Current population code intentionally rejects legacy population manifests unless historical replay is explicitly enabled with `VF_ALLOW_LEGACY_POPULATION_CHECKPOINT=1`. That compatibility opt-in is for intentional historical replay only.
+
+## Video relationship
+
+The recorded After playback used body v7 / environment v7, plasticity disabled during playback, and passed two gates under its historical evaluation condition. The playback was not a held-out evaluation, and task-triggered PAM stimulation remained enabled even though plasticity was off. The v966 checkpoint belongs to a mixed historical lineage assembled across more than one earlier development condition.
+
+This is a historical visualization result, not canonical v1 evidence. Canonical v1 frozen evaluation disables both plasticity and task-triggered DAN stimulation.
+
+The paired historical Before repository is [`../before`](../before).
+
+## Source code and reproducibility
+
+- Project overview: https://huggingface.co/shute2004/virtual-fly
+- GitHub source: https://github.com/shute2004/virtual-fly
+- Canonical package: https://github.com/shute2004/virtual-fly/tree/main/canonical/canonical-v1
+- Full artifact hash manifest: https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json
+
+The checkpoint is not self-contained without a compatible MaleCNS snapshot and the `virtual-fly` runtime. Raw MaleCNS is intentionally not mirrored here; obtain it from the official MaleCNS source or use the GitHub reproduction path.
+
+## Directory contents
+
+```text
+README.md
+ATTRIBUTION.md
+provenance.json
+SHA256SUMS
+checkpoint/
+  manifest.json
+  membrane.f32le
+  spikes.u32le
+  refractory.u32le
+  activity-trace.f32le
+  modulation.f32le
+  weights.f32le
+  eligibility.f32le
+```
+
+The checkpoint directory is kept in the native `virtual-fly` checkpoint layout so that the source repository can consume it without repacking. Raw MaleCNS source data and body assets are intentionally not included.
+
+## Integrity
+
+`SHA256SUMS` records the exact hashes of the original checkpoint files selected for publication. Verify the checkpoint before use.
+
+## License and upstream attribution
+
+The checkpoint artifact is distributed as **CC BY 4.0** because its weights derive from the CC BY 4.0 MaleCNS dataset. See `ATTRIBUTION.md`. Original `virtual-fly` source code and documentation remain MIT licensed.

checkpoints/historical-video/after/SHA256SUMS

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+  "schema_version": 3,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "step": 164754,
+  "global_weight_version": 966,
+  "membrane_file": "membrane.f32le",
+  "spikes_file": "spikes.u32le",
+  "refractory_file": "refractory.u32le",
+  "activity_trace_file": "activity-trace.f32le",
+  "modulation_file": "modulation.f32le",
+  "weights_file": "weights.f32le",
+  "eligibility_file": "eligibility.f32le"
+}

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checkpoints/historical-video/after/provenance.json

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+{
+  "schema_version": 1,
+  "artifact_id": "historical-video-after",
+  "lineage": "historical-video",
+  "historical": true,
+  "dataset": "male-cns:v1.0",
+  "neuron_count": 166700,
+  "edge_count": 25582938,
+  "global_weight_version": 966,
+  "source_locator": "artifacts/experiments/flyppy-v7h-online-video-v966/checkpoint",
+  "source_hash_manifest": "https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json",
+  "malecns_official_source": "https://male-cns.janelia.org/download/",
+  "malecns_license": "CC-BY-4.0",
+  "checkpoint_neural_step": 164754,
+  "checkpoint_semantics": "legacy-unspecified-in-manifest",
+  "mixed_historical_lineage": true,
+  "video_playback_source": "artifacts/experiments/flyppy-post-compare-final/after/playback.json",
+  "video_evaluation_plasticity": false,
+  "video_evaluation_task_triggered_pam_stimulation": true,
+  "video_evaluation_is_holdout": false,
+  "video_passed_gates": 2,
+  "repository": "shute2004/virtual-fly",
+  "path": "checkpoints/historical-video/after"
+}

checkpoints/historical-video/before/ATTRIBUTION.md

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+# Attribution and license
+
+The checkpoint weights in this checkpoint directory derive from the released MaleCNS `male-cns:v1.0` connectome. The official MaleCNS download page distributes that dataset under **Creative Commons Attribution 4.0 International (CC BY 4.0)**.
+
+- MaleCNS project: https://male-cns.janelia.org/
+- Official download: https://male-cns.janelia.org/download/
+- License: https://creativecommons.org/licenses/by/4.0/
+- Primary MaleCNS reference: Bates et al. (2026), *Distributed control circuits across a brain-and-cord connectome*, Nature.
+
+`virtual-fly` transforms the upstream connectome into a simulation checkpoint and, for trained/historical states, may contain subsequent locally computed synaptic-weight changes. This checkpoint artifact is therefore distributed as CC BY 4.0 and identifies it as a derived numerical state.
+
+Original `virtual-fly` source code and documentation are MIT licensed. No raw MaleCNS download, FlyBody asset, FlyGym source, or MuJoCo source is redistributed in this Hugging Face repository. Those upstream resources remain under their own licenses and should be obtained from their official projects.
+
+Detailed third-party notices: https://github.com/shute2004/virtual-fly/blob/main/THIRD_PARTY_NOTICES.md

checkpoints/historical-video/before/README.md

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+---
+license: cc-by-4.0
+language:
+  - en
+tags:
+  - drosophila
+  - connectome
+  - computational-neuroscience
+  - neuromodulation
+  - synaptic-plasticity
+  - virtual-fly
+  - checkpoint
+  - reproducible-research
+---
+
+# virtual-fly historical video Before checkpoint
+
+> **Lineage:** Historical Before-video state
+
+This directory contains the exact historical checkpoint used for the **Before** side of the published `virtual-fly` Before/After comparison video. It is intentionally separated from the current canonical initial checkpoint.
+
+Internal provenance: global weight version **240**, checkpoint neural step **26,224**, source experiment `flyppy-v7-envv7-frontier`. The public repository name deliberately omits `v240`; the version is retained here only as historical provenance.
+
+## Historical semantics
+
+This checkpoint predates the explicit current population-checkpoint contract: its original manifest does **not** declare `global-weights-only-v1` or current class-DAN provenance. It must not be silently relabeled as a canonical checkpoint. Current population code intentionally rejects legacy population manifests unless historical replay is explicitly enabled with `VF_ALLOW_LEGACY_POPULATION_CHECKPOINT=1`. That compatibility opt-in is for intentional historical replay only.
+
+## Video relationship
+
+The recorded Before playback used body v7 / environment v7, plasticity disabled during playback, and passed one gate under its historical evaluation condition. **This is not an untrained initial MaleCNS state:** v240 had already undergone 240 historical training episodes. The playback was not a held-out evaluation, and task-triggered PAM stimulation remained enabled even though plasticity was off. The historical lineage through v960 also used the older dopamine-source definition.
+
+These conditions are not equivalent to canonical v1 frozen evaluation, which disables both plasticity and task-triggered DAN stimulation.
+
+The paired historical After repository is [`../after`](../after).
+
+## Source code and reproducibility
+
+- Project overview: https://huggingface.co/shute2004/virtual-fly
+- GitHub source: https://github.com/shute2004/virtual-fly
+- Canonical package: https://github.com/shute2004/virtual-fly/tree/main/canonical/canonical-v1
+- Full artifact hash manifest: https://github.com/shute2004/virtual-fly/blob/main/release/huggingface/checkpoint-artifacts-v1.json
+
+The checkpoint is not self-contained without a compatible MaleCNS snapshot and the `virtual-fly` runtime. Raw MaleCNS is intentionally not mirrored here; obtain it from the official MaleCNS source or use the GitHub reproduction path.
+
+## Directory contents
+
+```text
+README.md
+ATTRIBUTION.md
+provenance.json
+SHA256SUMS
+checkpoint/
+  manifest.json
+  membrane.f32le
+  spikes.u32le
+  refractory.u32le
+  activity-trace.f32le
+  modulation.f32le
+  weights.f32le
+  eligibility.f32le
+```
+
+The checkpoint directory is kept in the native `virtual-fly` checkpoint layout so that the source repository can consume it without repacking. Raw MaleCNS source data and body assets are intentionally not included.
+
+## Integrity
+
+`SHA256SUMS` records the exact hashes of the original checkpoint files selected for publication. Verify the checkpoint before use.
+
+## License and upstream attribution
+
+The checkpoint artifact is distributed as **CC BY 4.0** because its weights derive from the CC BY 4.0 MaleCNS dataset. See `ATTRIBUTION.md`. Original `virtual-fly` source code and documentation remain MIT licensed.

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+  "spikes_file": "spikes.u32le",
+  "refractory_file": "refractory.u32le",
+  "activity_trace_file": "activity-trace.f32le",
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