scitex-agent-container 0.10.3

Declarative YAML-based framework for defining, managing, and orchestrating AI coding agent instances

scitex-agent-container

Declarative YAML-based AI agent lifecycle management

pip install scitex-agent-container

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Interfaces: Python ⭐⭐ · CLI ⭐⭐⭐ · MCP ⭐ · Skills ⭐⭐ · Hook — · HTTP —

Problem and Solution

#	Problem	Solution
1	Fragile per-agent scripts — launching Claude Code / Cursor / Aider means hand-rolling shell scripts for tmux, env vars, MCP configs, and auto-accept prompts, with no restart policy or health monitoring	Declarative YAML manifest — one file fully specifies runtime, model, MCP servers, env, health checks, and remote host; sac start brings the agent up in tmux/screen with auto-accept and a watchdog
2	No fleet story — scaling from one agent to many across machines duplicates the same fragile scripts, with no SSH deploy, no presence, and no inter-agent comms	Remote deploy + state inspection — sac copies src files, installs the venv over SSH, and keeps a live view of every pane's state so the fleet behaves as one unit

Problem

Managing AI coding agents (Claude Code, Cursor, Aider) in production requires manual script-writing, environment setup, and process monitoring for each agent instance. Scaling from one agent to a fleet across multiple machines means duplicating fragile shell scripts with no health checks, restart policies, remote deployment, or inter-agent communication.

Solution

scitex-agent-container provides declarative YAML definitions that fully specify an agent -- runtime, model, MCP servers, environment, health checks, remote host -- started with a single command:

YAML manifest + src_CLAUDE.md + src_mcp.json
          |
          v
scitex-agent-container start
          |
          v
tmux/screen session + auto-accept TUI prompts
                     + remote SSH deploy
                     + health monitor
                     + restart policy

Installation

Requires Python >= 3.10.

pip install scitex-agent-container

Templates

config/templates/ ships six minimal pattern templates — copy and adapt:

Template	Pattern	When to use
local.yaml	claude-code on local host	Default; shares operator's env (skills, MCP, venv)
docker.yaml	claude-code in Docker	Local isolation; mount_host_claude opt-in
apptainer.yaml	claude-code in Apptainer/Singularity	HPC compute nodes / locked-down hosts
ssh.yaml	claude-code via SSH on remote host	Cross-machine fleet member
ssh-slurm.yaml	SLURM-submitted job (with auto-resubmit)	Long-running compute on shared cluster
mcp.yaml	claude-code with MCP server wiring	Agent that needs MCP tool access

Concrete real-world configs live in config/examples/ (e.g. newbie-docker.yaml, researcher-opus.yaml). Both directories are validated by tests/test_templates_v3_valid.py — every shipped YAML must round-trip through load_config, and the SLURM template must additionally render a valid sbatch script.

To instantiate (dir-as-SSoT — agent name is derived from the parent directory):

mkdir -p ~/.scitex/orochi/agents/my-agent
cp config/templates/local.yaml ~/.scitex/orochi/agents/my-agent/my-agent.yaml
scitex-agent-container start my-agent

Quickstart (v2 config)

1. Create agent definition directory:

my-agent/
  my-agent.yaml     # Agent config
  src_CLAUDE.md      # -> deployed to {workdir}/CLAUDE.md
  src_mcp.json       # -> deployed to {workdir}/.mcp.json
  src_env            # -> deployed to {workdir}/.env  (mode 0600)

The src_* family is a generic file-deploy pipeline: a sibling file named src_X next to the YAML is materialized into the workspace at agent start, with ${VAR} and ${metadata.name} interpolation. src_env is the dotenv variant — sourceable by anything the agent spawns (cron jobs, ssh-launched commands, fresh shells), not just the multiplexer session. See _skills/scitex-agent-container/06_env-injection-ports.md for the four distinct env-injection ports and when to use each.

2. Write a YAML manifest:

apiVersion: scitex-agent-container/v2
kind: Agent
metadata:
  name: my-agent
  labels:
    role: worker
    machine: local
spec:
  runtime: claude-code
  model: sonnet
  multiplexer: tmux       # tmux (default) or screen

  claude:
    flags:
      - --dangerously-skip-permissions
    # session: continue-or-new (default) | continue | new
    # continue-or-new: pass --continue iff a prior session exists for the
    #   workdir, else launch fresh. Preserves /compact history across
    #   rolling restarts without risking a hard failure.
    # continue: always pass --continue (fails if no prior session)
    # new:      never pass --continue
    session: continue-or-new

  skills:
    required:
      - scitex

  health:
    enabled: true
    interval: 60
    method: multiplexer-alive

  restart:
    policy: on-failure
    max_retries: 3

v2 auto-derives from metadata.name: workdir, session name, env vars (CLAUDE_AGENT_ID, CLAUDE_AGENT_ROLE, etc.), and pre-start hooks. Sibling src_CLAUDE.md and src_mcp.json files are deployed to the workspace with ${metadata.name} and ${ENV_VAR} interpolation.

3. Start and monitor:

scitex-agent-container start my-agent.yaml
scitex-agent-container inspect my-agent         # Live state detection
scitex-agent-container status my-agent
scitex-agent-container logs my-agent -n 100
scitex-agent-container attach my-agent          # Ctrl-B D to detach (tmux)

Remote SSH Deployment

Deploy agents to remote machines:

spec:
  remote:
    host: mba              # SSH hostname
    user: ywatanabe
    timeout: 180

scitex-agent-container start remote-agent.yaml   # SSHs to remote, launches there
scitex-agent-container stop remote-agent.yaml     # Accepts name or YAML path
scitex-agent-container inspect my-remote-agent    # Live state from remote

SLURM (single-agent)

Submit an agent as an sbatch job that holds the allocation, runs claude in tmux on the compute node, and auto-resubmits before walltime via a SIGUSR1 trap:

spec:
  runtime: slurm
  slurm:
    partition: cascade
    cpus_per_task: 4
    mem: "16G"
    time_limit: "7-00:00:00"
    auto_resubmit: true
    hooks:
      pre_agent: ~/path/to/module-load.sh    # `module load Python/3.11.3` etc.

sac start head-spartan/head-spartan.yaml   # submits sbatch on the local SLURM submission host
sac attach head-spartan                    # srun --pty + tmux attach on the compute node
sac stop head-spartan                      # scancel + clear state

SLURM (multi-tenant — many agents on one allocation)

Requires pip install scitex-agent-container[slurm] (pulls scitex-hpc>=0.6.1).

Book a reservation once, then launch many agents into the same allocation. Cuts queue wait from minutes per launch to one ssh round-trip per launch:

# Once: book a node for the day
scitex-hpc reservations book dev-pool \
    --host spartan --partition cascade \
    --cpus 8 --mem 32G --time 7-0 \
    --tmux-server sac --persistent

# All day: launch agents into it
sac start dev-helper.yaml         # tmux session in dev-pool's allocation
sac start doc-builder.yaml        # second tmux session, same allocation
sac start test-runner.yaml        # third, same allocation

sac attach dev-helper             # interactive on compute node

# When done with the day's pool:
scitex-hpc reservations release dev-pool

Tenant agent YAML — note the new runtime kind and the slurm.reservation field:

spec:
  runtime: slurm-tenant
  slurm:
    reservation: dev-pool         # name of the existing scitex-hpc lease
  claude:
    flags: [--dangerously-skip-permissions]

The reservation's hold body bootstraps a long-lived tmux server as PID 1 of the sbatch script (via --tmux-server sac), so tenant tmux sessions survive past their setup commands. Without it, srun --overlap step cgroups would terminate them within seconds.

Compatible with HPC policies banning persistent daemons — every operation is bastion-initiated SSH, no crontab @reboot, no autossh, no tunnel. SLURM's documented SIGUSR1 signal handles walltime auto-resubmit.

MCP Servers (src_mcp.json)

MCP config lives alongside the YAML as src_mcp.json -- visible, editable, version-controlled:

{
  "mcpServers": {
    "scitex-orochi": {
      "type": "stdio",
      "command": "bun",
      "args": ["run", "~/proj/scitex-orochi/ts/mcp_channel.ts"],
      "env": {
        "SCITEX_OROCHI_URL": "wss://scitex-orochi.com",
        "SCITEX_OROCHI_AGENT": "${metadata.name}",
        "SCITEX_OROCHI_TOKEN": "${SCITEX_OROCHI_TOKEN}"
      }
    }
  }
}

~ in args is expanded at deploy time. ${metadata.name} interpolates from YAML. ${ENV_VAR} resolves from the environment.

Auto-Accept TUI Prompts

Claude Code shows confirmation prompts for dangerous flags. The auto-accept system handles them automatically using modular prompt handlers (runtimes/prompts.py):

# Each handler: detect prompt text -> send number key + Enter
PromptHandler(name="bypass-permissions",
              detect=lambda c: "2. Yes, I accept" in c,
              keys=["2", "Enter"])

Handlers are order-agnostic, use numbered option text for reliability, and work with both tmux and screen. New prompts are added by appending to PROMPT_HANDLERS.

Diagnostics logged to ~/.scitex/agent-container/logs/{name}/auto-accept.log.

CLI Commands

# Lifecycle (accepts name or YAML path)
scitex-agent-container start <config.yaml>
scitex-agent-container stop <name|yaml>
scitex-agent-container restart <name|yaml>

# Inspection
scitex-agent-container inspect <name> [--json]   # Live pane state detection
scitex-agent-container status [name] [--json]   # Rich status dict (see below)
scitex-agent-container list [--json] [--capability X] [--machine Y]
scitex-agent-container logs <name> [-n LINES]
scitex-agent-container health <name> [--json]
scitex-agent-container attach <name>

# Hook event ingestor (wired from Claude Code hooks, see below)
scitex-agent-container hook-event <pretool|posttool|prompt|stop|other>

# Pane actions (see "Pane Actions" below)
scitex-agent-container actions run <nonce-probe|compact> <agent> [--json]
scitex-agent-container actions query [--agent X] [--action Y] [--since 2h]
scitex-agent-container actions stats [--agent X] [--since 7d]
scitex-agent-container actions purge [--days N]

# A2A protocol — standalone agent endpoint, no fleet deps
# (echo handler by default; --handler claude_cli runs `claude --print`)
scitex-agent-container a2a serve <agent.yaml>... [--port 8888] [--handler echo|claude_cli|exec]

# Configuration
scitex-agent-container validate <config.yaml>
scitex-agent-container check <config.yaml>

# Maintenance
scitex-agent-container cleanup

Rich Status (status <name> --json)

status <name> --json returns a non-agentic snapshot of the agent suitable for dashboards or fleet monitors. The payload merges the base registry entry with fields from agent_meta.collect_rich() and event_log.summarize():

Field	Description
pane_text	Recent tmux capture-pane output, secrets redacted
pane_state	Classified: running / idle_prompt / y_n_prompt / auth_error / compose_pending_unsent / limit_reached / unknown
stuck_prompt_text	Last line when pane_state indicates a blocking prompt
claude_md	Workspace CLAUDE.md contents (truncated)
mcp_json	Workspace .mcp.json with token-like values redacted
recent_tools, recent_prompts	Last N tool uses / user prompts from the hook ring-buffer
agent_calls, background_tasks	Subagent launches and Bash run_in_background=true starts
tool_counts	{tool_name: count} over the window
last_tool_at, last_tool_name	ISO timestamp and name of the newest pretool event (any tool) -- functional heartbeat, distinguishes "process alive" from "LLM actually producing tool calls"
last_mcp_tool_at, last_mcp_tool_name	Same, restricted to tools whose name starts with mcp__ -- MCP sidecar health probe
last_action_at, last_action_name	ISO timestamp and name of the most recent PaneAction attempt. last_action_name (renamed from last_action) avoids a column collision with orochi's hub schema.
last_action_outcome, last_action_elapsed_s	Outcome (success, precondition_fail, send_error, completion_timeout, skipped_by_policy) and wall-clock duration of that attempt
action_counts	{action_name: count} rollup from action_store.summarize()
p95_elapsed_s_by_action	{action_name: p95_seconds} per-action latency headline
context_pct, current_tool, current_task, last_user_msg, model_transcript	Derived from the active Claude Code transcript JSONL
quota_5h_used_pct, quota_7d_used_pct, quota_*_reset_at	Claude usage (best-effort, cached)
metrics	Host-level CPU / memory / load / disk (psutil)

Every field is best-effort: failures leave the default value ("", 0, []) rather than raising.

scitex-agent-container status my-agent --json | jq '.pane_state, .recent_tools[-3:]'

Claude Code Hook Integration

hook-event is the non-agentic counterpart to the status command: Claude Code invokes it on every tool call / prompt / stop, and the handler appends a compact JSON record to a per-agent ring-buffer at $XDG_DATA_HOME/.scitex/agent-container/events/<agent>.jsonl (capped at 500 lines). status --json reads that buffer to populate recent_tools, recent_prompts, agent_calls, background_tasks, and tool_counts.

Wire it in the agent workspace's .claude/settings.local.json:

{
  "hooks": {
    "PreToolUse":       [{"matcher": "", "hooks": [
      {"type": "command", "command": "scitex-agent-container hook-event pretool"}
    ]}],
    "PostToolUse":      [{"matcher": "", "hooks": [
      {"type": "command", "command": "scitex-agent-container hook-event posttool"}
    ]}],
    "UserPromptSubmit": [{"matcher": "", "hooks": [
      {"type": "command", "command": "scitex-agent-container hook-event prompt"}
    ]}],
    "Stop":             [{"matcher": "", "hooks": [
      {"type": "command", "command": "scitex-agent-container hook-event stop"}
    ]}]
  }
}

Agent name resolution order: --agent <name> flag > SCITEX_OROCHI_AGENT env var > CLAUDE_AGENT_ID env var > basename of the current working directory. The handler swallows all errors so a broken log can never block a tool call.

Pane Actions

A typed, logged vocabulary for pane-mediated agent actions. Each action is a PaneAction subclass implementing four methods (snapshot / precheck / send / is_complete); the run_action engine classifies every attempt as success, precondition_fail, send_error, completion_timeout, or skipped_by_policy, and writes it to a host-wide SQLite log at ~/.scitex/agent-container/actions.db (agent is a column, not a path). Two concrete actions ship today:

• NonceProbeAction -- sends Repeat <nonce> and confirms the model echoes it back (true functional liveness, not just "process alive").
• CompactAction -- sends /compact and confirms by watching context_pct drop by at least --min-drop-pct (default 20).

# Run an attempt (non-zero exit on any non-SUCCESS / non-SKIPPED).
scitex-agent-container actions run nonce-probe <agent>
scitex-agent-container actions run compact <agent> \
    --min-drop-pct 30 --timeout 60 --json

# Query / aggregate / purge the attempt log.
scitex-agent-container actions query \
    --agent <agent> --action compact --since 2h --limit 20
scitex-agent-container actions stats --agent <agent> --since 7d
scitex-agent-container actions purge --days 14

The latest attempt is folded into status --json via agent_meta.collect_rich() as last_action_at / last_action_name / last_action_outcome / last_action_elapsed_s, with rollups action_counts and p95_elapsed_s_by_action.

Reliable send_keys into a running pane needs an inter-key delay and a settle window before Enter. Both are configurable via env vars (read once at import time by runtimes/tmux.py and runtimes/screen.py):

Env var	Default	Meaning
SCITEX_AGENT_KEY_DELAY_S	0.1	Delay between individual keys
SCITEX_AGENT_SUBMIT_SETTLE_S	0.3	Settle after text, before Enter
SCITEX_AGENT_ACTION_RETENTION_DAYS	30	Default actions purge --days horizon

A send_text_and_submit(session, text) helper wraps the "type then submit" pattern used by every action's send.

Zero Coupling to Downstream Orchestrators

scitex-agent-container is a generic library. It knows nothing about scitex-orochi, the hub, or any particular dashboard. status --json emits a self-describing dict; downstream consumers (e.g. orochi's heartbeat-push command) wrap it -- calling status --json, reshaping the payload, and POSTing to whatever endpoint they own. Keeping the two sides decoupled lets you swap the orchestrator, the transport, or the schema without touching this package.

YAML Spec Reference

Section	Key Fields	Description
apiVersion	scitex-agent-container/v2, cld-agent/v1	Config format version
metadata	name, labels	Agent identity and labels
spec.runtime	claude-code, cursor, aider	AI coding tool
spec.model	sonnet, opus[1m]	Model selection
spec.multiplexer	tmux (default), screen	Terminal multiplexer
spec.remote	host, user, timeout	SSH remote deployment
spec.claude	flags[], session, auto_accept	Claude Code options. session values: continue-or-new (default, try --continue with graceful fallback), continue (strict resume), new (always fresh). Top-level spec.session: also accepted and takes precedence.
spec.health	enabled, interval, method	Health monitoring
spec.restart	policy, max_retries, backoff	Auto-restart
spec.skills	required[], available[]	Skill injection
spec.env	key-value pairs	Environment variables
spec.venv	path	Python virtualenv to activate
spec.hooks	pre_start, post_start, pre_stop, post_stop	Lifecycle hooks
spec.container	runtime, image, volumes	Docker/Apptainer

Part of SciTeX

scitex-agent-container is part of SciTeX, used as a generic agent lifecycle library by downstream orchestrators like scitex-orochi for multi-machine fleet dispatch.

Four Freedoms for Research

0. The freedom to run your research anywhere -- your machine, your terms.
1. The freedom to study how every step works -- from raw data to final manuscript.
2. The freedom to redistribute your workflows, not just your papers.
3. The freedom to modify any module and share improvements with the community.

AGPL-3.0

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