SciTeX Agent Container (scitex-agent-container)

Declarative, on-prem-first lifecycle manager for autonomous agent processes.

One YAML spec → one reproducible, sandboxed, fleet-addressable agent.
Runs anywhere Apptainer runs — laptop, HPC node, air-gapped server.

Full Documentation · uv pip install scitex-agent-container[all]

Why sac

Installation

uv pip install "scitex-agent-container[all]"

Or via the SciTeX umbrella: uv pip install "scitex[agent-container]" → use as scitex agent-container ... (CLI) or import scitex.agent_container (Python).

Quickstart

Step 1 — Build the base image (one-time, ~5 min)

sac image build base

Step 2 — Create agent directories

# Each agent lives in its own directory; the directory name is the agent name.
mkdir -p ~/.scitex/agent-container/agents/hello-agent-{1,2}

Step 3 — Write spec.yaml (copy into each agent directory, adjust startup_prompts)

# ~/.scitex/agent-container/agents/hello-agent-1/spec.yaml
apiVersion: scitex-agent-container/v3
kind: Agent

spec:
  runtime: apptainer

  apptainer:
    image: ~/.scitex/agent-container/containers/sac-base.sif

  claude:
    model: haiku
    flags:
      - --dangerously-skip-permissions

  startup_prompts:
    - "Reply with the string 'Hello! I am hello-agent-1' and nothing else."

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

  restart:
    policy: never

Or copy the bundled example: cp -r examples/agents/hello-agent ~/.scitex/agent-container/agents/hello-agent-1

Step 4 — Run

# Start in foreground (waits for completion)
sac agents start hello-agent-1 hello-agent-2 --foreground

# Check status (fleet view)
sac agents status

# Start in background, send a follow-up turn, tail, stop, delete
sac agents start  hello-agent-1 hello-agent-2
sac agents send   hello-agent-1 "What is 2+2? Reply with just the number."
sac agents tail   hello-agent-1 hello-agent-2 --json
sac agents stop   hello-agent-1 hello-agent-2
sac agents delete hello-agent-1 hello-agent-2 -y

Tutorial

examples/ walks through the runtime in 15 lessons (image build, sandbox/update/freeze, versioning, run/send/tail, logs/exec, stop/remove, binds, env+user, writing your first spec.yaml, to_home/, A2A endpoint, health+restart, multi-host, debugging). Run them read-only with bash examples/00_run_all.sh, or --apply to execute the mutating ones. Pre-baked agent specs live in examples/agents/ (hello-agent, minimal-agent, full-agent, codex-agent, deepseek-agent, proxy-agent).

Which harnesses actually start

The harness registry has four entries, and spec.harness accepts three values. Only the anthropic ones can be started today — a registry entry is a declaration, not a working launch path, and this table says which is which rather than letting the count imply support that is not there:

A non-anthropic harness loads, validates and resolves to its registry entry, but every lifecycle launch path refuses it loudly rather than silently starting a Claude runner under a spec that asked for something else. The one working alternative today is spec.a2a.handler: openai_session for the OpenAI SDK; there is no equivalent A2A executor for codex yet.

spec.runtime only discriminates within the anthropic family — the openai and codex families have a single entry each, so the runtime axis selects nothing for them.

Models

spec.claude.model is the per-agent model knob. Be aware that sac resolves it to sonnet when a spec leaves it empty — for every agent, whichever harness the spec selects. That Anthropic-shaped default is real and not yet unwound by the harness/runtime/inference layering work.

Anthropic aliases:

Aliases auto-track the latest version of each family; append [1m] for the 1M-token context window (opus[1m], sonnet[1m]). Pin an exact build with a full ID like claude-opus-4-7 or claude-haiku-4-5-20251001.

A non-Anthropic inference endpoint? spec.claude.provider swaps the ENDPOINT, not the harness — the Claude-family harness keeps running, pointed somewhere else. Set spec.claude.provider: codex with a GPT model to use the local scitex-genai ChatGPT-subscription gateway. Other bundled entries are deepseek, mimo, and xiaomi; a dict { base_url: "...", auth_token_env: "..." } accepts any Anthropic-compatible endpoint. Under an override the model id is the endpoint's own (e.g. deepseek-chat), so the claude-* alias check relaxes and the table above no longer applies. Codex setup and multi-account configuration are documented in docs/credentials.md. See examples/agents/deepseek-agent/ for the generic provider shape. Full harness + model + provider reference →

How it works

sac materializes a spec.yaml into a long-lived, externally addressable agent process — whichever harness drives its turns:

  spec.yaml   ─┐
  to_home/    ─┴─→ sac agents start ──→ apptainer instance
                                          │
                                          ▼
                              long-lived harness session (TUI or SDK)
                              │
                              ├── <workdir>  (= spec.workdir, mounted rw)
                              ├── spec.mounts[]  ← host-path allowlist (ro/rw)
                              ├── state-dir  (~/.scitex/agent-container/runtime/<name>/)
                              └─→ POST /v1/turn  (per-agent A2A inbound)

SAC-from-SAC (in-SIF spawn). An agent running INSIDE an apptainer SIF can spawn a child agent on the bare host by calling sac agents start <child> as normal — the CLI auto-detects the in-SIF condition (APPTAINER_CONTAINER) and POSTs the spawn RPC to the host's sac listen instead of trying nested apptainer (which the supported HPC shape forbids). The host re-runs ACL gating, records the parent → child lineage, and shells the real start against the bare host's apptainer. Wiring is automatic: SAC_LISTEN_BASE_URL + SAC_LISTEN_BEARER are injected at container launch.

Full architecture → — launch flow, to_home merge rules, A2A inbound, control plane, restart/health.

YAML Spec Reference (v3) → — annotated full example + field table (apiVersion, spec.harness, spec.runtime, spec.apptainer., spec.claude., a2a, health, restart, provider).

Talking to a Running Agent → — three transports (A2A POST /v1/turn, sac agents send, host-level sac listen), when to use which, copy-pasteable curl examples.

Container Isolation → — 10 Apptainer-default leak paths + sac's hardened-by-default countermeasures (--containall auto-prepended, opt-out via spec.apptainer.relaxed: true). The reference for reproducibility claims.

Configuration and Runtime Directories

Full directory reference → — complete tree, configuration cascade (CLI flag → env var → project config → user config).

~/.scitex/agent-container/
├── agents/<name>/spec.yaml    ← agent definition (SSoT)
├── containers/sac-base.sif    ← built images (gitignored)
└── runtime/<name>/            ← live state: pid, heartbeat, session.jsonl

Apptainer images → — base vs scitex layers, sandbox/freeze workflow, version pinning.

Host listen as a persistent service

sac listen is the host's HTTP/JSON control plane (push hub, spawn broker, lead inbox). For long-running deployments install the bundled systemd-user unit so it auto-starts on boot and auto-restarts on crash:

install -m 0644 scripts/systemd/sac-listen.service ~/.config/systemd/user/
systemctl --user daemon-reload
systemctl --user enable --now sac-listen.service
journalctl --user -u sac-listen.service -n 50          # logs
curl -s http://127.0.0.1:7878/v1/health                # healthcheck

See scripts/systemd/README.md for the full recipe + the federated-jobs vs hand-maintained-services split.

Three Interfaces

# Agent lifecycle
sac agents start  <name> [--foreground]   # daemon by default; --foreground streams stdio
                                           # inside a SIF: auto-brokers to host listen
                                           # (no apptainer-in-apptainer needed)
sac agents stop   <name>                  # graceful SIGTERM, escalate to SIGKILL after 5 s
                                           # --force tolerates an unreachable bound host
sac agents restart <name>
sac agents delete <name>                  # stop + remove spec dir + runtime dir + registry
sac agents forget <name> [--force]        # local-only state.db cleanup for the
                                           # "agent is gone, only stale rows persist" case
                                           # (no ssh, no signal)
sac agents send   <name> "<prompt>"       # send a follow-up turn to a running session
sac agents send   <name> --key ESC        # interrupt current turn
sac agents status [<name>] [--snapshot] [--priority]   # FLEET-WIDE view if no name;
                                                       # per-agent JSON payload otherwise
sac agents list   [<name>]                # alias of `status` (same renderer)
sac agents list   --host <hostname>       # one host; repeatable, exact match.
                                           # `localhost` is resolved at parse time and
                                           # the header echoes the resolution.
                                           # The fleet view ALWAYS prints a header saying
                                           # which hosts answered and which did not, with
                                           # the reason ("5/6 hosts responded — spartan:
                                           # ssh timed out after 8s"). A host that could
                                           # not be reached is REPORTED, never dropped:
                                           # `agents: []` means an EMPTY fleet only when
                                           # `hosts.responded == hosts.total` in --json.
sac agents health <name>
sac agents tail   <name>                  # render session.jsonl (structured transcript)
sac agents recall <name>                  # human-readable session summary
sac agents check  <name>                  # preflight (validates yaml + probes runtime deps)
sac agents find   <capability>            # search by metadata.labels.capabilities

# Control plane (HTTP/JSON, loopback-only)
sac listen [--bind 127.0.0.1:7878]        # boot per-host REST API (bearer-auth)
                                           # single-instance flock guard fails loud
                                           # on a duplicate launch (PID + lockfile shown)
sac listen restart                        # atomic stop-clean-relaunch
sac peer post-turn <to> "<msg>"           # local agent-to-agent message via sac listen
sac peer resolve-url <to>                 # print URL post-turn would target

# A2A protocol (generic, no fleet deps)
sac a2a serve <yamls...>                  # inbound HTTP for non-SDK runtimes
                                           # (apptainer-runtime agents host /v1/turn themselves)
sac a2a doctor <agent>                    # probe AgentCard endpoint
sac a2a grant / revoke / block / unblock / grants

# Image lifecycle (delegates to scitex-container)
sac image build [base|scitex] [--sandbox]
sac image sandbox SOURCE                  # SIF → writable sandbox
sac image update  SANDBOX [-p PKG]        # pip install --upgrade
sac image freeze  SANDBOX OUT.sif         # sandbox → SIF
sac image list                            # installed versions
sac image switch  VERSION                 # atomic flip
sac image rollback                        # restore previous
sac image status                          # unified dashboard
sac image snapshot [-o env.json]          # reproducibility capsule

# Accounts / quota (multi-account rotation)
sac accounts list / save / delete / switch        # stored-credential rotation
sac accounts status                       # one-shot quota snapshot (5h%, 7d%, tier)
sac accounts quota                        # this agent's own live quota
sac accounts refresh                      # mint fresh access_token from refresh_token
sac accounts sync-live / watch-live       # auto-snapshot live cred on `claude /login`
sac accounts watch-quota                  # auto-rotate when quota threshold hit

# Network / peers
sac host list / add / remove / set / probe / exec / validate
sac host ssh-opts                         # print sac's ssh ControlMaster flags (shell-quoted)
sac host add-peer / list-peers / remove-peer      # cross-host listen-bearer registry
sac host probe-hub                        # WSL → fleet-hub layered connectivity probe

# Fleet (peer-aware multi-agent orchestration)
sac fleet launch  PEER <name>...          # rsync specs to PEER, start each remotely
sac fleet notify  done|blocker|status --summary "..."   # agent→lead push (ADR-0013)
sac fleet sync                            # cross-host spec audit (fails loud on drift)

# Diagnostics / introspection
sac doctor [--fleet]                      # diagnose agent-spec source drift
sac subagent get-state                    # Claude Code Agent-tool subagent state
sac mcp list-tools                        # MCP introspection
sac skills list / get                     # bundled agent-facing skills

# Federated scheduled jobs (delegates to scitex-dev ecosystem)
sac dev systemd list / install / uninstall    # kind=timer|service -> ~/.config/systemd/user/sac.*
sac dev cron    list / install / uninstall    # kind=cron -> crontab entries

# State db / registry / events
sac db query / show / clean / export / import / migrate / tick   # state.db inspection
sac registry sync / reconcile             # cross-host comms_nodes anti-entropy
sac event ingest                          # Claude Code hook event ingestor

# Misc
sac installation boot                     # first-time host bootstrap (venv, PATH, cron)
sac list-python-apis                      # enumerate public Python API
sac --help-recursive                      # full subcommand tree

# Direct import
import scitex_agent_container as sac

cfg = sac.load_config("~/.scitex/agent-container/agents/hello-agent-1/spec.yaml")
sac.validate_config(cfg)
sac.agent.start("hello-agent-1")           # daemon
sac.agent.status("hello-agent-1")          # dict matching `sac agents status --json`
sac.peer.post_turn("hello-agent-1", "What is 2+2?")

# Or via the umbrella
import scitex
scitex.agent_container.agent.start("hello-agent-1")

spec:
  mcp_servers:
    filesystem:
      command: npx
      args: ["-y", "@modelcontextprotocol/server-filesystem", "/work"]

Part of SciTeX

scitex-agent-container is part of SciTeX. Install via the umbrella with pip install scitex[agent-container] to use as scitex.agent_container (Python) or scitex agent-container ... (CLI).

An external fleet hub can add cross-host message routing, a chatops UI, and a peer registry on top of sac. The dependency is one-way — the hub reads sac's on-disk state and published HTTP endpoints; sac never imports it. See docs/adr/0008-sac-node-transport-boundary.md for the transport boundary sac guarantees.

Four Freedoms for Research

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 — because we believe research infrastructure deserves the same freedoms as the software it runs on.