From f6102650ac912a630d8e81964478b92be59c734d Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Mon, 9 Mar 2026 02:14:49 +0000
Subject: [PATCH] Add ruv-neural-cli README

https://claude.ai/code/session_01DGUAowNScGVp88bK2eiuRv
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+# rUv Neural CLI
+
+CLI tool for the rUv Neural brain topology analysis system. Provides commands for
+simulating neural sensor data, analyzing brain connectivity graphs, computing
+minimum cuts, running full analysis pipelines, and exporting results to multiple
+visualization formats.
+
+## Installation
+
+```bash
+cargo install --path .
+```
+
+Or build from the workspace root:
+
+```bash
+cargo build -p ruv-neural-cli --release
+```
+
+The binary is named `ruv-neural`.
+
+## Command Reference
+
+| Command    | Description                                           |
+|------------|-------------------------------------------------------|
+| `simulate` | Generate simulated multi-channel neural sensor data   |
+| `analyze`  | Load and analyze a brain connectivity graph (JSON)    |
+| `mincut`   | Compute minimum cut (Stoer-Wagner or multi-way)       |
+| `pipeline` | Full end-to-end: simulate -> filter -> graph -> decode|
+| `export`   | Export brain graph to D3, DOT, GEXF, CSV, or RVF     |
+| `info`     | Show system info, crate versions, and capabilities    |
+
+## Usage Examples
+
+### Simulate Neural Data
+
+Generate 64-channel simulated neural data at 1 kHz for 10 seconds:
+
+```bash
+ruv-neural simulate -c 64 -d 10.0 -s 1000.0 -o output.json
+```
+
+Default parameters (no arguments required):
+
+```bash
+ruv-neural simulate
+```
+
+### Analyze a Brain Graph
+
+Load a graph from JSON and display topology metrics:
+
+```bash
+ruv-neural analyze -i brain_graph.json
+```
+
+With ASCII adjacency matrix visualization:
+
+```bash
+ruv-neural analyze -i brain_graph.json --ascii
+```
+
+Export per-node metrics to CSV:
+
+```bash
+ruv-neural analyze -i brain_graph.json --csv metrics.csv
+```
+
+### Compute Minimum Cut
+
+Standard two-way Stoer-Wagner minimum cut:
+
+```bash
+ruv-neural mincut -i brain_graph.json
+```
+
+Multi-way cut with 4 partitions:
+
+```bash
+ruv-neural mincut -i brain_graph.json -k 4
+```
+
+### Run Full Pipeline
+
+The pipeline command runs all stages end-to-end:
+
+1. Generate simulated sensor data
+2. Preprocess (bandpass filter 1-100 Hz)
+3. Construct brain connectivity graph (PLV)
+4. Compute minimum cut and topology metrics
+5. Generate topology and spectral embeddings
+6. Decode cognitive state
+7. Display results summary
+
+```bash
+ruv-neural pipeline -c 32 -d 5.0
+```
+
+With ASCII dashboard visualization:
+
+```bash
+ruv-neural pipeline -c 16 -d 3.0 --dashboard
+```
+
+### Export Graph
+
+Export to D3.js-compatible JSON:
+
+```bash
+ruv-neural export -i brain_graph.json -f d3 -o graph.d3.json
+```
+
+Export to Graphviz DOT:
+
+```bash
+ruv-neural export -i brain_graph.json -f dot -o graph.dot
+```
+
+All supported formats:
+
+```bash
+ruv-neural export -i graph.json -f d3   -o out.json   # D3.js JSON
+ruv-neural export -i graph.json -f dot  -o out.dot    # Graphviz DOT
+ruv-neural export -i graph.json -f gexf -o out.gexf   # GEXF XML
+ruv-neural export -i graph.json -f csv  -o out.csv    # CSV edge list
+ruv-neural export -i graph.json -f rvf  -o out.rvf    # RuVector File
+```
+
+### System Info
+
+```bash
+ruv-neural info
+```
+
+### Verbosity
+
+Use `-v` flags for increased logging detail:
+
+```bash
+ruv-neural -v pipeline -c 8 -d 2.0      # INFO level
+ruv-neural -vv pipeline -c 8 -d 2.0     # DEBUG level
+ruv-neural -vvv pipeline -c 8 -d 2.0    # TRACE level
+```
+
+## Output Formats
+
+| Format | Extension | Description                                    |
+|--------|-----------|------------------------------------------------|
+| D3     | `.json`   | D3.js force-directed graph with nodes and links|
+| DOT    | `.dot`    | Graphviz DOT for rendering with `dot` or `neato`|
+| GEXF   | `.gexf`   | Graph Exchange XML Format for Gephi            |
+| CSV    | `.csv`    | Edge list with source, target, weight, metric  |
+| RVF    | `.json`   | RuVector File format with adjacency matrix     |
+
+## Pipeline Walkthrough
+
+The `pipeline` command demonstrates the full rUv Neural analysis flow:
+
+```
+simulate -> filter -> PLV graph -> mincut -> embed -> decode
+```
+
+**Step 1 - Simulate**: Generates multi-channel neural data with alpha (10 Hz),
+beta (20 Hz), and gamma (40 Hz) oscillations plus white noise.
+
+**Step 2 - Filter**: Applies a 4th-order Butterworth bandpass filter (1-100 Hz)
+using zero-phase SOS filtering.
+
+**Step 3 - Graph**: Computes Phase Locking Value (PLV) between all channel pairs
+and constructs a brain connectivity graph with edges above a PLV threshold.
+
+**Step 4 - Mincut**: Runs the Stoer-Wagner algorithm for the global minimum cut,
+revealing the natural partition boundary in the brain network.
+
+**Step 5 - Embed**: Generates both topology-based and spectral (Laplacian
+eigenvector) embeddings of the brain graph state.
+
+**Step 6 - Decode**: Classifies the cognitive state (Rest, Focused, MotorPlanning)
+using a threshold decoder on topology metrics.
+
+**Step 7 - Results**: Displays a formatted summary table with all computed metrics.