Cleanup before network implementation

.gitignore

@@ -21,6 +21,9 @@ analysis/.venv/
 # Data — raw CSVs committed, processed outputs not
 data/**/*_processed.csv
 
+# Self-signed dev TLS material — regenerate with `make certs`
+certs/
+
 # OS
 .DS_Store
 *.swp

CLAUDE.md

@@ -0,0 +1,112 @@
+# quic_ecs_dt — Project Guide for Claude
+
+## What & why
+
+Source repo for **"QUIC + ECS as Complementary Transport and Runtime Substrates for Industrial Digital Twins"** — UCAmI 2026 (Plantevin & Francillette, UQAC). Third paper in a sequence; the first two are at IEEE SWC 2026:
+
+- `plantevin2026ecs` — ECS as runtime substrate for industrial DT (200k assets @ 114 Hz on Pi 5).
+- `plantevin2026quic` — QUIC partial reliability for DT sensor streams (94% P99 reduction vs TCP at 5% loss).
+
+**UCAmI hypothesis (the composition question):** prior work shows ECS and QUIC each work as substrates *independently*. Does integrating real QUIC traffic into a Bevy ECS ingest path introduce coupling that degrades either one's claimed properties? The paper argues no, and measures it.
+
+## Architecture
+
+Three-tier QUIC ↔ ECS bridge, headless Bevy runtime:
+
+| Tier | QUIC primitive | Use case | Channel cap |
+|------|----------------|----------|-------------|
+| T1 | Unreliable datagrams (RFC 9221) | High-freq ephemeral telemetry; drops OK | 1024, lossy backpressure |
+| T2 | Unidirectional streams | Ordered threshold events; reliable | 512, fully drained |
+| T3 | Bidirectional streams | Actuator commands w/ ACK | 256, fully drained |
+
+QUIC server runs on a dedicated OS thread with a Tokio multi-thread runtime; pushes decoded `QuicMessage` (UUID + stream_id + f64 + ts + seq) into `tokio::sync::mpsc` per tier; Bevy `IngestSystem` drains in `PreUpdate`. Pattern is in [substrate/src/transport/ecs.rs](substrate/src/transport/ecs.rs).
+
+**Target hardware:** CM5 (BCM2712, Cortex-A76, 4 GB) as DT runtime; M4 Max as traffic generator; 1 Gbps direct Ethernet. Both rigs are in hand.
+
+## Repo map
+
+```
+quic_ecs_dt/
+├── paper/                Quarto + LNCS source — single index.qmd, refs in references.bib
+├── substrate/            Rust crate: Bevy 0.18 + Quinn 0.11 + rustls 0.23 + Tokio
+│   └── src/
+│       ├── main.rs       App::new, MinimalPlugins, EcsQuicTransportPlugin
+│       ├── config.rs     figment chain: defaults → config.toml → APP_* env
+│       └── transport/
+│           ├── mod.rs    QuicMessage struct
+│           ├── ecs.rs    Plugin: tokio thread + 3 mpsc + PreUpdate ingest
+│           └── server.rs run_substrate_server (EMPTY STUB)
+├── simulator/            Rust crate: stub today; will be Quinn client + Bevy sensor generators
+├── data/                 (created by M6) loopback/, two_machine/ — raw CSVs committed, *_processed ignored
+├── Cargo.toml            workspace
+└── Makefile              render, preview, build, build-cm5, deploy-cm5
+```
+
+## Status
+
+| Area | State |
+|------|-------|
+| `AppConfig` figment loader (defaults → TOML → env) | Done — [substrate/src/config.rs:42](substrate/src/config.rs#L42) |
+| 3-tier MPSC bridge scaffolding (Tokio thread + Bevy plugin) | Done — [substrate/src/transport/ecs.rs](substrate/src/transport/ecs.rs) |
+| `QuicMessage` struct (no codec yet) | Defined — [substrate/src/transport/mod.rs:4](substrate/src/transport/mod.rs#L4) |
+| Quinn server (accept loop, demux, decode) | **Empty stub** — [substrate/src/transport/server.rs:4](substrate/src/transport/server.rs#L4) |
+| TLS / self-signed cert | Done (M1) — `certs/server.{crt,key}` via `make certs`, gitignored |
+| Wire codec for `QuicMessage` (38 B fixed LE) | Done (M1) — [substrate/src/transport/mod.rs:35](substrate/src/transport/mod.rs#L35); 4 unit tests passing |
+| `tracing-subscriber` init w/ `RUST_LOG` | Done (M1) — [substrate/src/main.rs:8-12](substrate/src/main.rs#L8-L12) |
+| ECS components (`RawSensorData`) + 5 systems (Ingest/Sim/Export/FaultInjection/Diagnostics) | Missing — placeholder at [substrate/src/transport/ecs.rs:26](substrate/src/transport/ecs.rs#L26) |
+| VictoriaMetrics + Grafana export | Missing |
+| Simulator (Quinn client + sensor generators) | `Hello, world!` — [simulator/src/main.rs](simulator/src/main.rs) |
+| `config.toml` at repo root | Done (M1) — [config.toml](config.toml); loaded by [substrate/src/main.rs:9](substrate/src/main.rs#L9) |
+| Benchmark harness (sweep + CSV writer) | Missing |
+| CM5 cross-compile / deploy | Wired in [Makefile:30](Makefile#L30); not exercised |
+
+`cargo run -p substrate` boots, prints the loaded config, and idles on the (still-empty) Quinn server. `MinimalPlugins` busy-loops the ECS schedule by default — expected, will gate to `tick_rate_hz` in M4.
+
+## Roadmap
+
+Each milestone has one verification gate. Update Status here as we go.
+
+- **M1 — Wire codec & root config.** ✅ Done 2026-05-04. Hand-rolled little-endian codec on `QuicMessage` (38 B fixed: 16 UUID + 2 stream_id + 8 f64 + 8 ts_us + 4 seq) with roundtrip + layout + length-error tests; `config.toml` at repo root; dev TLS via `make certs`; structured `tracing-subscriber` init reads `RUST_LOG` (default `info`).
+- **M2 — Quinn server + self-signed TLS.** Fill [substrate/src/transport/server.rs](substrate/src/transport/server.rs): `Endpoint::server`, accept loop, demux T1=datagrams / T2=uni / T3=bi, push into matching `mpsc::Sender`. Use `rcgen` for a dev cert at boot. *Verify:* a Quinn smoke client connects, server logs handshake.
+- **M3 — Simulator client.** Replace [simulator/src/main.rs](simulator/src/main.rs) with a Bevy app: Quinn client, N synthetic devices, configurable per-tier rates. *Verify:* end-to-end loopback drains messages on all three tiers.
+- **M4 — ECS world.** Define `RawSensorData` and the 5 systems the paper names (`FaultInjectionSystem`, `IngestSystem`, `SimulationSystem`, `ExportSystem`, `DiagnosticsSystem`). Wire `IngestSystem` into the existing `PreUpdate` slot. *Verify:* with 10k simulated devices, entity count stabilizes; `DiagnosticsSystem` logs steady tick rate.
+- **M5 — Observability (VictoriaMetrics + Grafana).** Substrate exposes Prometheus-format `/metrics` (use `metrics` + `metrics-exporter-prometheus`): tick rate, RSS, per-tier P50/P99/P999, channel depth, drop count. Commit a Grafana dashboard JSON. *Verify:* `curl :PORT/metrics` returns labeled samples; dashboard renders against VM.
+- **M6 — Benchmark harness.** Sweep `entity_count ∈ {10k, 50k, 100k, 200k}` × `loss_rate ∈ {0%, 1%, 5%}` with 2k warmup + 5k measurement ticks. Loss via `tc netem` or in-app injection. Writes `data/loopback/final_table.csv`. *Verify:* one full sweep on M4 Max produces a CSV the Quarto figures consume.
+- **M7 — CM5 cross-compile & deploy.** Exercise [Makefile:30](Makefile#L30) (`build-cm5`, `deploy-cm5`); set real `CM5_HOST`. *Verify:* binary runs on CM5 with a feed from M4 Max over 1 Gbps Ethernet.
+- **M8 — Two-machine run + paper render.** Sweep with simulator on M4 Max → substrate on CM5; populate `data/two_machine/final_table.csv`; `make render` produces a PDF. **Update §Evaluation prose to reflect actual numbers.** Current paper figures (241 Hz, 64 µs / 15.8 ms P99, 2.6 µs jitter, 1.02 MB/1k, R²=0.9999) are **aspirational placeholders** — they may move and the conclusions may shift; that's expected.
+
+## Conventions
+
+- **Rust:** edition 2024; workspace at root with `simulator` + `substrate`; `opt-level=1` dev, `opt-level=3` for deps.
+- **Pinned crates:** Bevy 0.18, Quinn 0.11, rustls 0.23, Tokio 1 (full), figment 0.10 (toml + env), uuid 1.23 (v4), serde 1.
+- **Config:** `figment` chain — defaults in [substrate/src/config.rs:25](substrate/src/config.rs#L25) → `config.toml` → env `APP_*` (double-underscore for nesting, e.g. `APP_NETWORK__SERVER_PORT=9000`).
+- **Bevy:** headless — `MinimalPlugins` only; do not pull rendering plugins.
+- **Tokio↔Bevy:** keep the dedicated-thread + mpsc pattern in [substrate/src/transport/ecs.rs:49](substrate/src/transport/ecs.rs#L49); do not block the ECS schedule on async work.
+- **Paper:** Quarto + LNCS template ([paper/_extensions/template.tex](paper/_extensions/template.tex), [paper/_quarto.yml](paper/_quarto.yml)). **Never commit `llncs.cls` or `splncs04.bst`** — CTAN licensing; download per [README.md:25-34](README.md#L25-L34).
+- **Data:** raw CSVs under `data/` are committed; `*_processed.csv` is gitignored. Paper figures consume `data/loopback/final_table.csv` and `data/two_machine/final_table.csv`.
+- **Build artifacts:** `target/`, `paper/_output/`, `paper/figures/`, `paper/.quarto/`, `paper/index.tex` all gitignored.
+
+## Run / verify
+
+```bash
+make certs              # generate certs/server.{crt,key} (ECDSA P-256, SAN: localhost/cm5.local/127.0.0.1/::1)
+make build              # cargo build --release (native, depends on certs)
+make build-cm5          # aarch64 cross-build for the CM5 (depends on certs)
+make deploy-cm5         # scp to $CM5_HOST (set in env or override Makefile var)
+make render             # build the paper PDF
+make preview            # live-reload paper preview at :4848
+make clean              # cargo clean + drop generated paper outputs
+```
+
+`certs/` is gitignored; `make build` regenerates the dev cert if missing. From the repo root: `cargo run -p substrate` boots, prints the loaded `AppConfig`, and idles. `config.toml` and cert paths are resolved relative to the cwd — always launch from the repo root.
+
+## Key references
+
+- Prior self-citations: `plantevin2026ecs`, `plantevin2026quic` (both IEEE SWC 2026, "to appear").
+- QUIC: RFC 9000 (core), RFC 9221 (unreliable datagrams).
+- DT foundations: Tao et al. 2019; Grieves & Vickers 2017; Minerva et al. 2020.
+- ECS: Nystrom 2014, *Game Programming Patterns*.
+- Mixed-reliability transport: Peeck et al. (W2RP for DDS).
+- DT sync metrics: Çakır et al. 2023 (Twin Alignment Ratio); Bellavista et al. 2023 (ODTE).
+- Industrial QUIC/IIoT: Fernández et al. 2021; Boeding et al. 2025.
+- Full bibliography: [paper/references.bib](paper/references.bib).

Makefile

@@ -8,7 +8,7 @@
 #    make clean       — remove generated outputs
 # ============================================================
 
-.PHONY: render preview build build-cm5 clean
+.PHONY: render preview build build-cm5 clean certs
 
 VENV        := $(HOME)/.venv/quic_ecs
 PYTHON      := $(VENV)/bin/python
@@ -16,6 +16,22 @@ CM5_HOST    ?= 192.168.1.x
 CM5_USER    ?= pi
 CM5_BIN_DIR ?= /home/pi/quic_ecs_dt
 
+# Self-signed dev TLS for the QUIC server (regenerate with `make certs`).
+# SAN covers loopback, ::1, and cm5.local for the two-machine setup.
+CERT_DIR  := certs
+CERT_FILE := $(CERT_DIR)/server.crt
+KEY_FILE  := $(CERT_DIR)/server.key
+
+certs: $(CERT_FILE)
+
+$(CERT_FILE):
+	mkdir -p $(CERT_DIR)
+	openssl req -x509 -newkey ec -pkeyopt ec_paramgen_curve:P-256 \
+	    -keyout $(KEY_FILE) -out $(CERT_FILE) \
+	    -days 3650 -nodes \
+	    -subj "/CN=localhost/O=quic_ecs_dt-dev/OU=substrate" \
+	    -addext "subjectAltName=DNS:localhost,DNS:cm5.local,IP:127.0.0.1,IP:::1"
+
 # Paper
 render:
 	cd paper && quarto render index.qmd
@@ -23,11 +39,11 @@ render:
 preview:
 	cd paper && quarto preview index.qmd --port 4848 --no-browser
 
-# Rust build
+# Rust build (depends on dev cert so `cargo run` boots out of the box)
-build:
+build: $(CERT_FILE)
 	cargo build --release
 
-build-cm5:
+build-cm5: $(CERT_FILE)
 	CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER=aarch64-linux-gnu-gcc \
 	cargo build --release --target aarch64-unknown-linux-gnu
 

config.toml

@@ -0,0 +1,18 @@
+# quic_ecs_dt — substrate runtime config
+#
+# Resolution order (figment chain in substrate/src/config.rs):
+#   1. compile-time defaults
+#   2. this file
+#   3. APP_* env vars  (e.g. APP_NETWORK__SERVER_PORT=9001)
+#
+# All paths are resolved relative to the cwd at launch — run from the repo root.
+
+[network]
+server_port      = 9000
+server_interface = "0.0.0.0"
+server_cert      = "certs/server.crt"
+server_key       = "certs/server.key"
+
+[simulation]
+tick_rate_hz = 60
+max_entities = 10000

substrate/Cargo.toml

@@ -7,7 +7,8 @@ edition = "2024"
 bevy = "0.18"
 thiserror = "2"
 anyhow = "1"
-tracing-subscriber = "0.3"
+tracing = "0.1"
+tracing-subscriber = { version = "0.3", features = ["env-filter"] }
 quinn = { version = "0.11" }
 rustls = { version = "0.23" }
 tokio = { version = "1", features = ["full"] }

substrate/src/config.rs

@@ -20,6 +20,7 @@ pub struct QuicConfig {
     pub server_port: u16,
     pub server_interface: String,
     pub server_cert: String,
+    pub server_key: String,
 }
 
 impl Default for AppConfig {
@@ -28,7 +29,8 @@ impl Default for AppConfig {
             network : QuicConfig {
                 server_port: 9000,
                 server_interface: "0.0.0.0".to_string(),
-                server_cert: "cert.pem".to_string(),
+                server_cert: "certs/server.crt".to_string(),
+                server_key: "certs/server.key".to_string(),
             },
             simulation: SimulationConfig {
                 tick_rate_hz: 60,

substrate/src/main.rs

@@ -1,17 +1,23 @@
 mod transport;
 mod config;
 
-use std::sync::Arc;
 use bevy::prelude::*;
+use tracing_subscriber::EnvFilter;
 use crate::config::AppConfig;
 
 fn main() {
+    tracing_subscriber::fmt()
+        .with_env_filter(
+            EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info")),
+        )
+        .init();
+
     let config = AppConfig::load("config.toml").expect("Failed to load config");
-    println!("{:?}", config);
+    tracing::info!(?config, "substrate starting");
 
     App::new()
         .insert_resource(config)
         .add_plugins(MinimalPlugins)
-        .add_plugins(transport::ecs::EcsQuicTransportPlugin{})
+        .add_plugins(transport::ecs::EcsQuicTransportPlugin {})
         .run();
 }

substrate/src/transport/ecs.rs

@@ -1,7 +1,6 @@
-use std::sync::{Arc, Mutex};
+use std::sync::Mutex;
 use bevy::prelude::*;
 use tokio::sync::mpsc;
-use crate::config::QuicConfig;
 use crate::transport::QuicMessage;
 use crate::transport::server::run_substrate_server;
 

substrate/src/transport/mod.rs

@@ -1,11 +1,126 @@
 pub mod ecs;
 mod server;
 
+/// One sensor sample on the wire.
+///
+/// Fixed 38-byte little-endian layout — same on x86_64 and aarch64 (the two
+/// evaluation hosts), so encode/decode is effectively a memcpy.
+///
+/// ```text
+///   offset  size  field
+///   ------  ----  --------------------------
+///        0    16  device_id          (UUID)
+///       16     2  data_stream_id     (u16)
+///       18     8  raw_value          (f64)
+///       26     8  timestamp_us       (u64)
+///       34     4  sequence_number    (u32)
+/// ```
 #[derive(Debug, Clone, Default, Copy, PartialEq)]
-pub struct QuicMessage{
+pub struct QuicMessage {
     pub device_id: uuid::Uuid,
     pub data_stream_id: u16,
     pub raw_value: f64,
     pub timestamp_us: u64,
     pub sequence_number: u32,
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum WireError {
+    #[error("expected exactly {expected} bytes, got {got}")]
+    BadLength { expected: usize, got: usize },
+}
+
+impl QuicMessage {
+    /// Bytes on the wire — fixed-size, no length prefix.
+    pub const WIRE_SIZE: usize = 38;
+
+    pub fn encode_to(&self, buf: &mut [u8]) -> Result<(), WireError> {
+        if buf.len() != Self::WIRE_SIZE {
+            return Err(WireError::BadLength {
+                expected: Self::WIRE_SIZE,
+                got: buf.len(),
+            });
+        }
+        buf[0..16].copy_from_slice(self.device_id.as_bytes());
+        buf[16..18].copy_from_slice(&self.data_stream_id.to_le_bytes());
+        buf[18..26].copy_from_slice(&self.raw_value.to_le_bytes());
+        buf[26..34].copy_from_slice(&self.timestamp_us.to_le_bytes());
+        buf[34..38].copy_from_slice(&self.sequence_number.to_le_bytes());
+        Ok(())
+    }
+
+    pub fn to_bytes(&self) -> [u8; Self::WIRE_SIZE] {
+        let mut buf = [0u8; Self::WIRE_SIZE];
+        self.encode_to(&mut buf).expect("WIRE_SIZE buffer is exactly sized");
+        buf
+    }
+
+    pub fn decode(buf: &[u8]) -> Result<Self, WireError> {
+        if buf.len() != Self::WIRE_SIZE {
+            return Err(WireError::BadLength {
+                expected: Self::WIRE_SIZE,
+                got: buf.len(),
+            });
+        }
+        let mut id_bytes = [0u8; 16];
+        id_bytes.copy_from_slice(&buf[0..16]);
+        Ok(Self {
+            device_id: uuid::Uuid::from_bytes(id_bytes),
+            data_stream_id: u16::from_le_bytes(buf[16..18].try_into().unwrap()),
+            raw_value: f64::from_le_bytes(buf[18..26].try_into().unwrap()),
+            timestamp_us: u64::from_le_bytes(buf[26..34].try_into().unwrap()),
+            sequence_number: u32::from_le_bytes(buf[34..38].try_into().unwrap()),
+        })
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn wire_size_matches_fields() {
+        assert_eq!(QuicMessage::WIRE_SIZE, 16 + 2 + 8 + 8 + 4);
+    }
+
+    #[test]
+    fn roundtrip_preserves_all_fields() {
+        let msg = QuicMessage {
+            device_id: uuid::Uuid::from_u128(0x0123456789abcdef_fedcba9876543210),
+            data_stream_id: 0xBEEF,
+            raw_value: -273.15,
+            timestamp_us: 1_700_000_000_000_001,
+            sequence_number: 42,
+        };
+        let bytes = msg.to_bytes();
+        assert_eq!(bytes.len(), QuicMessage::WIRE_SIZE);
+        let decoded = QuicMessage::decode(&bytes).unwrap();
+        assert_eq!(msg, decoded);
+    }
+
+    #[test]
+    fn decode_rejects_wrong_length() {
+        assert!(matches!(
+            QuicMessage::decode(&[0u8; 37]),
+            Err(WireError::BadLength { expected: 38, got: 37 })
+        ));
+        assert!(matches!(
+            QuicMessage::decode(&[0u8; 39]),
+            Err(WireError::BadLength { expected: 38, got: 39 })
+        ));
+    }
+
+    #[test]
+    fn encode_layout_is_little_endian() {
+        let msg = QuicMessage {
+            device_id: uuid::Uuid::nil(),
+            data_stream_id: 0x0102,
+            raw_value: 0.0,
+            timestamp_us: 0,
+            sequence_number: 0x04030201,
+        };
+        let bytes = msg.to_bytes();
+        assert_eq!(&bytes[16..18], &[0x02, 0x01]);
+        assert_eq!(&bytes[34..38], &[0x01, 0x02, 0x03, 0x04]);
+    }
+}