Add autonomous Python agent system with Discord bot integration

Convert all 9 .claude/agents/*.md definitions to standalone Python agents
using the Claude Agent SDK, with a Discord bot replacing Slack for
bidirectional simulation operations.

New spectre_agents package:
- 9 agent classes mirroring .md agents (orchestrator, workflow-runner,
  stdout-diagnostics, model-output-review, namelist-validator,
  forcing-data-qc, dashboard-manager, notify, web-research)
- 8 tool modules (bash, file_io, slurm, mitgcm, forcing, namelist,
  dashboard, discord_notify)
- Discord bot with slash commands (/run, /diagnose, /review, /validate,
  /qc, /dashboard, /ensemble, /config)
- Interactive decision views (buttons) for orchestrator halting triggers
- Systemd service for daemon deployment on Spectre cluster
- Complete setup documentation in docs/discord-setup.md

https://claude.ai/code/session_01WNamUYvvru6xmxpPLqqW4f

Author: claude

docs/discord-setup.md

@@ -0,0 +1,244 @@
+# SPECTRE Agent System — Complete Setup Guide
+
+This guide covers setting up the autonomous Python agent system with Discord bot integration on the Spectre (Franklin) cluster.
+
+## Prerequisites
+
+- Python 3.11+ on the cluster login/utility node
+- `uv` package manager installed
+- Access to SLURM commands (`sbatch`, `sacct`, `squeue`)
+- BeeGFS mounted at `/mnt/beegfs/`
+- An Anthropic API key with access to Claude Opus 4.6, Sonnet 4.6, and Haiku 4.5
+- A Discord account with permission to create bots
+
+---
+
+## Step 1: Create a Discord Bot
+
+1. Go to https://discord.com/developers/applications
+2. Click **New Application** and name it `SPECTRE Bot`
+3. Go to the **Bot** tab:
+   - Click **Add Bot** (if not already created)
+   - Copy the **Token** — save it securely, you'll need it later
+   - Enable **Message Content Intent** (required for reading messages)
+   - Enable **Server Members Intent**
+4. Go to the **OAuth2 → URL Generator** tab:
+   - **Scopes**: select `bot` and `applications.commands`
+   - **Bot Permissions**: select:
+     - Send Messages
+     - Embed Links
+     - Attach Files
+     - Use Slash Commands
+     - Read Message History
+     - Create Public Threads
+   - Copy the generated URL
+5. Open the URL in your browser and add the bot to your Discord server
+
+## Step 2: Set Up Discord Server Channels
+
+Create these channels in your Discord server:
+
+| Channel | Purpose |
+|---------|---------|
+| `#simulation-status` | Automated status updates, milestones |
+| `#decisions` | Interactive decision requests with buttons |
+| `#alerts` | Failure alerts and critical warnings |
+| `#plots` | Surface field PNGs, convergence plots |
+| `#logs` | Verbose agent activity (optional) |
+
+**Get your Guild (Server) ID:**
+- Enable Developer Mode in Discord (Settings → Advanced → Developer Mode)
+- Right-click your server name → Copy Server ID
+
+## Step 3: Configure Secrets
+
+Create the secrets file on the cluster:
+
+```bash
+sudo mkdir -p /etc/spectre-agents
+sudo tee /etc/spectre-agents/env << 'EOF'
+ANTHROPIC_API_KEY=sk-ant-your-key-here
+DISCORD_BOT_TOKEN=your-bot-token-here
+DISCORD_GUILD_ID=your-guild-id-here
+EOF
+sudo chmod 600 /etc/spectre-agents/env
+sudo chown joe:joe /etc/spectre-agents/env
+```
+
+## Step 4: Install the Agent System
+
+```bash
+cd /mnt/beegfs/spectre-150-ensembles
+
+# Create virtual environment
+uv venv .venv
+
+# Install dependencies (includes spectre_agents package)
+uv sync
+
+# Verify the package loads
+.venv/bin/python -c "from spectre_agents.config import load_config; print('OK')"
+```
+
+## Step 5: Test the Bot Locally
+
+Before installing as a service, test interactively:
+
+```bash
+cd /mnt/beegfs/spectre-150-ensembles
+
+# Source the secrets
+source /etc/spectre-agents/env
+export ANTHROPIC_API_KEY DISCORD_BOT_TOKEN DISCORD_GUILD_ID
+
+# Run the agent system
+.venv/bin/python -m spectre_agents --config spectre_agents_config.yaml
+```
+
+You should see:
+```
+SPECTRE Agent System starting...
+Bot connected as SPECTRE Bot#1234 (ID: ...)
+Synced commands to guild ...
+```
+
+In Discord, the bot should post "SPECTRE Agent System online" in `#simulation-status`.
+
+Test slash commands:
+- `/run status` — should show current (idle) status
+- `/validate` — should run namelist validation
+- `/dashboard status` — should check dashboard health
+
+Press `Ctrl+C` to stop.
+
+## Step 6: Install as a Systemd Service
+
+```bash
+# Copy the service file
+sudo cp systemd/spectre-agents.service /etc/systemd/system/
+
+# Reload systemd
+sudo systemctl daemon-reload
+
+# Enable and start the service
+sudo systemctl enable spectre-agents
+sudo systemctl start spectre-agents
+
+# Check status
+sudo systemctl status spectre-agents
+
+# View logs
+journalctl -u spectre-agents -f
+```
+
+## Step 7: Verify Everything Works
+
+1. In Discord, run `/run status` — bot should respond with a status embed
+2. Run `/validate` — should trigger namelist validation and return results
+3. Run `/dashboard status` — should report dashboard component health
+4. Run `/run start` — should validate, submit a SLURM job, and start monitoring
+
+---
+
+## Architecture Overview
+
+```
+┌─────────────────────────────────────────────┐
+│           Spectre Cluster Node              │
+│                                             │
+│  systemd: spectre-agents.service            │
+│  ┌───────────────────────────────────────┐  │
+│  │  python -m spectre_agents             │  │
+│  │                                       │  │
+│  │  Discord Bot (asyncio event loop)     │  │
+│  │    ├── Slash commands → Agent runner  │  │
+│  │    ├── Decision queue ← Orchestrator  │  │
+│  │    └── Status embeds → Discord        │  │
+│  │                                       │  │
+│  │  Agent Runner (ThreadPoolExecutor)    │  │
+│  │    ├── Orchestrator (Opus)            │  │
+│  │    │   delegates to:                  │  │
+│  │    ├── WorkflowRunner (Haiku)         │  │
+│  │    ├── StdoutDiagnostics (Sonnet)     │  │
+│  │    ├── ModelOutputReview (Sonnet)     │  │
+│  │    ├── NamelistValidator (Sonnet)     │  │
+│  │    ├── ForcingDataQC (Sonnet)         │  │
+│  │    ├── DashboardManager (Haiku)       │  │
+│  │    ├── DiscordNotifier (Haiku)        │  │
+│  │    └── WebResearch (Sonnet)           │  │
+│  └───────────────────────────────────────┘  │
+│                                             │
+│  SLURM ←→ sbatch/sacct/squeue              │
+│  BeeGFS ←→ /mnt/beegfs/spectre-*           │
+│  Tailscale ←→ Dashboard proxy               │
+└─────────────────────────────────────────────┘
+```
+
+## Discord Commands Reference
+
+| Command | Description |
+|---------|-------------|
+| `/run start` | Validate config, submit simulation, start monitoring |
+| `/run status` | Show job state, model days, CFL, throughput |
+| `/run stop` | Cancel SLURM job, stop monitoring |
+| `/run resubmit` | Clear run dir, resubmit from pickup |
+| `/diagnose [job_id]` | Run STDOUT failure diagnostics |
+| `/review` | Model output physical plausibility check |
+| `/validate` | Pre-flight namelist validation |
+| `/qc forcing` | EXF forcing data QC |
+| `/qc obc` | OBC boundary data QC |
+| `/dashboard start` | Start monitoring stack |
+| `/dashboard status` | Health-check all components |
+| `/dashboard restart [component]` | Restart dashboard/converter/plotter |
+| `/ensemble start` | Begin bred vector generation |
+| `/ensemble status` | Show ensemble convergence |
+| `/config [param]` | Show simulation configuration |
+
+## Agent Autonomy Levels
+
+The system operates with **high autonomy**:
+
+**Autonomous actions (no Discord approval needed):**
+- Resubmit after SLURM walltime exceeded
+- Restart dead dashboard/plotter/converter processes
+- Clear run directory before resubmit
+- Rebuild container image if not found
+
+**Requires Discord approval (posts interactive buttons):**
+- Timestep changes (CFL approaching 0.45)
+- Ambiguous failure with multiple fix options
+- Physics parameter changes (viscosity, diffusion)
+- First-time configuration submission
+- Bred vector cycle completion review
+
+## Troubleshooting
+
+### Bot doesn't respond to commands
+- Check `journalctl -u spectre-agents -f` for errors
+- Verify `DISCORD_BOT_TOKEN` and `DISCORD_GUILD_ID` are correct
+- Ensure the bot has the required permissions in your server
+- Commands may take up to 1 hour to sync globally; guild sync is instant
+
+### "Claude Agent SDK not found" error
+- Ensure `claude-agent-sdk` is installed: `.venv/bin/pip list | grep claude`
+- The Claude Code CLI must be installed on the system: `which claude`
+
+### Agent times out
+- Check `ANTHROPIC_API_KEY` is valid and has quota
+- Increase `max_turns` in `spectre_agents_config.yaml` if agents need more steps
+- Check network connectivity from the cluster node
+
+### SLURM commands fail
+- Verify the service runs as the correct user (joe)
+- Check that SLURM is accessible from the node running the service
+- Ensure the working directory exists: `/mnt/beegfs/spectre-150-ensembles`
+
+## Cost Estimates
+
+| Agent | Model | Approx. cost per invocation |
+|-------|-------|---------------------------|
+| Orchestrator | Opus 4.6 | $0.10 – $0.50 |
+| Diagnostics/Review/Validator/QC | Sonnet 4.6 | $0.02 – $0.10 |
+| WorkflowRunner/Dashboard/Notify | Haiku 4.5 | $0.005 – $0.02 |
+
+A typical run-diagnose-fix-restart cycle costs approximately $0.50 – $1.00.

pyproject.toml

@@ -33,11 +33,17 @@ dependencies = [
   "xarray==2025.6.1",
   "xgcm==0.8.1",
   "zarr==3.0.8",
-  "MetPy==1.7.1"
+  "MetPy==1.7.1",
+  "claude-agent-sdk",
+  "discord.py>=2.3.0",
+  "anyio>=4.0.0",
 ]
 [project.urls]
 Homepage = "https://github.com/ocean-spectre/spectra-150-ensembles"
 Issues = "https://github.com/fluidnumerics/spectre_utils/issues"
 
+[project.scripts]
+spectre-agents = "spectre_agents.__main__:cli"
+
 [tool.setuptools]
-packages = ["spectre_utils"]
+packages = ["spectre_utils", "spectre_agents", "spectre_agents.tools", "spectre_agents.agents", "spectre_agents.discord_bot"]

spectre_agents/__init__.py

@@ -0,0 +1,7 @@
+"""SPECTRE Simulation Agent System.
+
+Autonomous Python agents for MITgcm ocean simulation orchestration,
+with Discord bot integration for bidirectional communication.
+"""
+
+__version__ = "0.1.0"

spectre_agents/__main__.py

@@ -0,0 +1,105 @@
+"""Entry point for the SPECTRE agent system.
+
+Usage:
+    python -m spectre_agents [--config PATH]
+
+Starts the Discord bot and agent runner as concurrent asyncio tasks.
+"""
+
+from __future__ import annotations
+
+import argparse
+import asyncio
+import logging
+import signal
+import sys
+from pathlib import Path
+
+from spectre_agents.config import load_config
+from spectre_agents.context import AgentContext
+from spectre_agents.discord_bot.bot import run_bot
+from spectre_agents.tools.discord_notify import set_agent_context
+
+logger = logging.getLogger("spectre_agents")
+
+
+def setup_logging() -> None:
+    """Configure structured logging to stderr and optional file."""
+    fmt = logging.Formatter(
+        "%(asctime)s [%(levelname)s] %(name)s: %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    handler = logging.StreamHandler(sys.stderr)
+    handler.setFormatter(fmt)
+
+    root = logging.getLogger()
+    root.setLevel(logging.INFO)
+    root.addHandler(handler)
+
+    # Suppress noisy discord.py debug logs
+    logging.getLogger("discord").setLevel(logging.WARNING)
+    logging.getLogger("discord.http").setLevel(logging.WARNING)
+
+
+async def main(config_path: str | None = None) -> None:
+    """Main async entry point."""
+    setup_logging()
+
+    config = load_config(config_path)
+    logger.info("Loaded config: base_dir=%s, sim_dir=%s", config.base_dir, config.sim_dir)
+
+    # Validate required secrets
+    if not config.anthropic_api_key:
+        logger.error("ANTHROPIC_API_KEY not set. Set it in /etc/spectre-agents/env or environment.")
+        sys.exit(1)
+    if not config.discord_bot_token:
+        logger.error("DISCORD_BOT_TOKEN not set. Set it in /etc/spectre-agents/env or environment.")
+        sys.exit(1)
+
+    # Initialize shared context
+    ctx = AgentContext(base_dir=config.base_dir)
+    ctx.load_state()
+    logger.info("Loaded state: status=%s, job=%s", ctx.simulation.status, ctx.simulation.active_job_id)
+
+    # Wire up Discord tools with the context
+    set_agent_context(ctx)
+
+    # Handle shutdown signals
+    loop = asyncio.get_event_loop()
+    stop_event = asyncio.Event()
+
+    def signal_handler(sig):
+        logger.info("Received signal %s, shutting down...", sig)
+        stop_event.set()
+
+    for sig in (signal.SIGINT, signal.SIGTERM):
+        loop.add_signal_handler(sig, signal_handler, sig)
+
+    # Run the Discord bot — it manages the event loop
+    logger.info("Starting SPECTRE Agent System...")
+    try:
+        await run_bot(config, ctx)
+    except asyncio.CancelledError:
+        pass
+    finally:
+        ctx.save_state()
+        logger.info("SPECTRE Agent System stopped.")
+
+
+def cli() -> None:
+    """CLI entry point."""
+    parser = argparse.ArgumentParser(
+        description="SPECTRE Simulation Agent System with Discord bot"
+    )
+    parser.add_argument(
+        "--config",
+        type=str,
+        default=None,
+        help="Path to spectre_agents_config.yaml",
+    )
+    args = parser.parse_args()
+    asyncio.run(main(args.config))
+
+
+if __name__ == "__main__":
+    cli()