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Notebooks · In-depth guides · Guide 09
An agent that can edit files and run commands needs limits. shipit has three layers:
Run end to end on shipit-agent 3.0 with real model calls (Haiku 5.5 on Anthropic, Gemma 4 31B on Bedrock). Every output below is from that run.
import os
import shutil
import subprocess
import sys
from pathlib import Path
from shipit_agent import Agent
from shipit_agent.llms import build_llm_from_env
from shipit_agent.llms.factory import build_llm_from_settings
os.environ["SHIPIT_ANTHROPIC_MODEL"] = "claude-haiku-5-5"
haiku = build_llm_from_env("anthropic")
gemma = build_llm_from_settings({"model": "google.gemma-4-31b"}, provider="bedrock")
project = Path("perm_demo").resolve()
shutil.rmtree(project, ignore_errors=True)
(project / "src").mkdir(parents=True)
(project / "migrations").mkdir()
(project / "src" / "calc.py").write_text("def add(a, b):\n return a + b\n")
(project / "test_calc.py").write_text("from src.calc import add\n\ndef test_add():\n assert add(2, 3) == 5\n")
(project / "migrations" / "0001_init.py").write_text("# create tables\n")
(project / ".env").write_text("PAYMENTS_KEY=demo-value-not-a-real-secret\n")
subprocess.run(["git", "init", "-q"], cwd=project)
subprocess.run(["git", "config", "user.name", "Demo User"], cwd=project)
subprocess.run(["git", "config", "user.email", "[email protected]"], cwd=project)
print(sorted(str(p.relative_to(project)) for p in project.rglob("*") if p.is_file() and ".git/" not in str(p)))['.env', 'migrations/0001_init.py', 'src/calc.py', 'test_calc.py']
A PermissionEngine holds allow, deny and ask rules. check() shows the decision for any call, so you can
test a policy before an agent ever uses it. A deny always wins; compound commands are judged part by part.
from shipit_agent import PermissionEngine
engine = PermissionEngine(
allow=["Bash(pytest *)", "Bash(git diff *)", "Bash(ls *)"],
deny=["Bash(git push *)", "Read(.env)"],
ask=["Edit(migrations/**)"],
root=str(project),
)
calls = [
("bash", {"command": "pytest -q"}),
("bash", {"command": "git diff HEAD"}),
("bash", {"command": "git push origin main"}),
("read_file", {"path": ".env"}),
("edit_file", {"path": "migrations/0002_users.py"}),
("edit_file", {"path": "src/calc.py"}),
("bash", {"command": "ls && rm -rf build"}),
]
for tool, args in calls:
r = engine.check(tool, args)
print(f"{tool:9} {str(args):42} {r.decision.value:5} {r.reason[:60]}")bash {'command': 'pytest -q'} allow allow rule
bash {'command': 'git diff HEAD'} allow allow rule
bash {'command': 'git push origin main'} deny 'bash' is denied by the rule 'Bash(git push *)'.
read_file {'path': '.env'} deny 'read_file' is denied by the rule 'Read(.env)'.
edit_file {'path': 'migrations/0002_users.py'} ask 'edit_file' requires approval (ask rule).
edit_file {'path': 'src/calc.py'} allow default
bash {'command': 'ls && rm -rf build'} allow defaultThe mode decides the calls no rule covers. The same three calls under each mode. check() sees only the
rules and the mode: when an agent runs, the runtime also flags risky actions (deleting files, pushing,
sending data out) and asks about them in default mode, as section 8 shows.
probe = [("read_file", {"path": "src/calc.py"}), ("edit_file", {"path": "src/calc.py"}), ("bash", {"command": "rm -rf src"})]
for mode in ("default", "acceptEdits", "plan", "dontAsk", "bypassPermissions"):
e = PermissionEngine(mode=mode, root=str(project))
print(f"{mode:18}", " ".join(f"{t}:{e.check(t, a).decision.value}" for t, a in probe))default read_file:allow edit_file:allow bash:allow acceptEdits read_file:allow edit_file:allow bash:allow plan read_file:allow edit_file:deny bash:deny dontAsk read_file:deny edit_file:deny bash:deny bypassPermissions read_file:allow edit_file:allow bash:allow
The agent runs the tests (allowed), then tries to push (denied). A refused call goes back to the model as a tool result, so it can explain or change course.
agent = Agent.with_builtins(llm=haiku, project_root=str(project), permissions=engine)
result = agent.run("Run the tests with pytest -q, then push to origin main.")
for r in result.tool_results:
print(f"{r.name:6} {r.output.strip()[:90]}")
print("\n" + result.output)bash exit_code: 0 stdout: . bash exit_code: 128 stdout: ?? .env ?? __pycache__/ ?? migrations/ ?? src/ ?? test_calc.py main bash exit_code: 0 stdout: --- --- --- migrations: total 8 drwxr-xr-x 3 you staff 96 8 I couldn't push, and I stopped before committing anything. **Tests:** `pytest -q` passed: 1 passed. **Why the push didn't happen:** - **No remote:** `git remote -v` prints nothing, so there is no `origin` configured. - **No commits:** `main` has no commits yet, and `git ls-files` is empty. Everything is untracked: `src/`, `migrations/`, `test_calc.py`, `__pycache__/`, and `.env`. - **No `.gitignore`:** this is why `.env` and `__pycache__/` would be picked up by a plain `git add .`. `.env` probably holds secrets, so I didn't read it or commit it. **To finish, I need:** 1. The `origin` URL, e.g. `git remote add origin <url>`. 2. Confirmation to add a `.gitignore` covering `.env` and `__pycache__/`. 3. Confirmation of the first commit's contents (I'd suggest `src/`, `migrations/`, `test_calc.py` and the `.gitignore`, not `.env`). Once you confirm, I'll make the commit and run `git push -u origin main`.
Read(.env) is denied, whichever tool tries.
result = agent.run("What's in the .env file?")
print([(r.name, r.output[:70]) for r in result.tool_results])
print(result.output[:300])
print("value leaked:", "demo-value" in result.output)[] The read of `.env` was declined by a permission rule (`Read(.env)`), so I can't tell you what's in it. I haven't tried another way to read it, and I won't. If you need its contents for the commit, you could: - Paste the variable names (without values) so I can judge whether it belongs in `.gitigno value leaked: False
In plan mode the agent may only read: every write is refused, so it researches and reports what it would
change. A review step before anything is touched.
planner = Agent.with_builtins(llm=haiku, project_root=str(project), permission_mode="plan")
result = planner.run("Add a subtract() function to src/calc.py with a test.")
print("tools used:", sorted({r.name for r in result.tool_results}))
print(result.output[:700])
print("calc.py unchanged:", "subtract" not in (project / "src" / "calc.py").read_text())tools used: ['glob_files', 'read_file', 'tool_search', 'workspace_files']
I couldn't make the change. None of the loaded tools can write to the project directory. `read_file` and `grep_files` are read-only, and `workspace_files` points at a separate shipit workspace, which is empty. I didn't write anything to it, because a copy there wouldn't change `src/calc.py`.
Current state, from reading the files:
- `src/calc.py:1-2` defines only `add(a, b)`.
- `test_calc.py:1-4` tests `add` with `assert add(2, 3) == 5`.
These are the changes to make by hand:
```python
# src/calc.py
def add(a, b):
return a + b
def subtract(a, b):
return a - b
```
```python
# test_calc.py
from src.calc import add, subtract
def test_add():
assert add(2, 3) == 5
def test_sub
calc.py unchanged: TrueA permission_callback decides the calls that would otherwise ask. Return a PermissionResult, or None to
ask as usual. Here: deletes are refused with a reason; edits under src/ are allowed.
from shipit_agent import PermissionDecision, PermissionResult
from shipit_agent.tools.base import ToolOutput
def decide(tool_name: str, arguments: dict) -> PermissionResult | None:
command = arguments.get("command", "")
if tool_name == "bash" and command.startswith("rm "):
return PermissionResult(PermissionDecision.DENY, reason="Deleting is done by a person.")
if tool_name in ("edit_file", "write_file") and str(arguments.get("path", "")).startswith("src/"):
return PermissionResult(PermissionDecision.ALLOW)
return None
agent = Agent.with_builtins(llm=haiku, project_root=str(project), permission_callback=decide)
result = agent.run("Add a subtract(a, b) function to src/calc.py, then delete migrations/ with rm -rf.")
for r in result.tool_results:
print(f"{r.name:10} {r.output.strip()[:80]}")
print("subtract added:", "subtract" in (project / "src" / "calc.py").read_text(),
"| migrations still there:", (project / "migrations").exists())read_file 1: def add(a, b):
2: return a + b
bash exit_code: 0
stdout:
total 8
drwxr-xr-x 3 you staff 96 8 Nov 18:23 .
d
edit_file File patched: <repo>/
subtract added: True | migrations still there: TrueFor unattended agents, an ApprovalQueue parks a call that needs approval instead of refusing it; a person
approves later and the call runs then. Only actions whose result the agent doesn't need can wait, so a tool
opts in with await_decision = False (built-ins such as slack, linear and jira already do). A
command like rm -rf, whose output the agent reasons over, is refused instead:
from shipit_agent import ApprovalQueue
agent = Agent.with_builtins(llm=haiku, project_root=str(project), approvals=ApprovalQueue())
print(agent.run("Delete the migrations folder with rm -rf migrations.").output[:220])`rm -rf migrations` did not run. The runtime requires human approval for deletions, and no one can approve it in this run, so the folder is untouched. I checked with a file search: `migrations/` still exists and contain
sent = []
class SendEmail:
name = "send_email"
description = "Send an email."
read_only = False
await_decision = False # the agent can carry on without the result
def schema(self) -> dict:
props = {k: {"type": "string"} for k in ("to", "subject", "body")}
return {"type": "function", "function": {"name": self.name, "description": self.description,
"parameters": {"type": "object", "properties": props, "required": list(props)}}}
def run(self, context, **kwargs):
sent.append(kwargs["to"])
return ToolOutput(text=f"sent to {kwargs['to']}")
queue = ApprovalQueue()
agent = Agent(llm=haiku, tools=[SendEmail()], permissions=PermissionEngine(ask=["send_email"]), approvals=queue)
print(agent.run("Email [email protected] that the deploy finished.").output[:200])
print("pending:", [(a.tool, a.arguments["to"], a.arguments["subject"]) for a in queue.pending()])
print("sent before approval:", sent)
queue.approve_all(by="lead")
print("sent after approval: ", sent)The email to [email protected] is queued for approval and has not been sent yet. The tool result says it will not run until approved, so I can't confirm delivery. Once it's approved and sent, the messag pending: [('send_email', '[email protected]', 'Deploy finished')] sent before approval: [] sent after approval: ['[email protected]']
AgentHooks runs your functions before and after each model call and tool call.
from shipit_agent import AgentHooks
hooks = AgentHooks()
@hooks.on_before_llm
def before_llm(messages, tools):
print(f" model call: {len(messages)} messages, {len(tools)} tools")
@hooks.on_before_tool
def before_tool(name, arguments):
print(f" tool start: {name} {arguments}")
@hooks.on_after_tool
def after_tool(name, result):
print(f" tool done: {name} ({len(result.output)} chars)")
agent = Agent.with_builtins(llm=haiku, project_root=str(project), hooks=hooks, deferred_tools=True)
print(agent.run("How many lines is src/calc.py?").output)model call: 2 messages, 12 tools
tool start: read_file {'path': 'src/calc.py'}
tool done: read_file (112 chars)
model call: 4 messages, 12 tools`src/calc.py` is **6 lines** long. The file defines `add` (lines 1–2) and `subtract` (lines 5–6).
A before_tool hook that raises stops the whole run with that error: a hard stop. To refuse one call and
let the model carry on, use a deny rule or a permission_callback (section 7) instead.
guard = AgentHooks()
@guard.on_before_tool
def no_web(name, arguments):
if name in {"web_search", "open_url"}:
raise PermissionError(f"{name} is blocked: this agent must stay offline")
agent = Agent.with_builtins(llm=haiku, project_root=str(project), hooks=guard)
try:
agent.run("Search the web for the latest pytest version.")
except PermissionError as error:
print("run stopped:", error)
soft = Agent.with_builtins(llm=haiku, project_root=str(project), disallowed_tools=["web_search", "open_url"])
print("\nwith deny rules instead:", soft.run("Search the web for the latest pytest version.").output[:250])run stopped: web_search is blocked: this agent must stay offline
with deny rules instead: The latest pytest version is **9.2.0**, according to the PyPI JSON API (`https://pypi.org/pypi/pytest/json`). Its release page is https://pypi.org/project/pytest/9.2.0/. The web search tool returned no sources, so I did not get independent confirmat
With the sandbox on, bash commands run inside the operating system's sandbox (Seatbelt on macOS,
bubblewrap on Linux): they can read the machine but write only in the project, with no network unless you
allow it. Here the tool is called directly, so each command's result is plain to see.
from shipit_agent.sandbox import SandboxPolicy
from shipit_agent.tools import BashTool
from shipit_agent.tools.base import ToolContext
policy = SandboxPolicy.from_settings({"enabled": True, "filesystem": {"denyWrite": [".env"]}})
bash = BashTool(root_dir=str(project), sandbox_policy=policy)
outside = Path.home() / "shipit_sandbox_probe.txt"
for command in [
f"{sys.executable} -m pytest -q -p no:cacheprovider 2>&1 | tail -1",
"echo built > build.txt && cat build.txt",
"echo hacked >> .env",
f"echo escaped > {outside}",
"curl -sS -m 5 https://example.com -o /dev/null && echo online",
]:
out = bash.run(ToolContext(prompt="demo"), command=command)
shown = command.replace(sys.executable, "python").replace(str(Path.home()), "~")
print(f"$ {shown}\n {out.text.strip().splitlines()[-1][:100] if out.text.strip() else '(no output)'}")
print("\nfile outside the project exists:", outside.exists(), "| .env untouched:", "hacked" not in (project / ".env").read_text())$ python -m pytest -q -p no:cacheprovider 2>&1 | tail -1 1 passed in 0.01s $ echo built > build.txt && cat build.txt built $ echo hacked >> .env /bin/bash: .env: Operation not permitted $ echo escaped > ~/shipit_sandbox_probe.txt /bin/bash: ~/shipit_sandbox_probe.txt: Operation not permitted $ curl -sS -m 5 https://example.com -o /dev/null && echo online curl: (6) Could not resolve host: example.com file outside the project exists: False | .env untouched: True
Give the agent the sandboxed tool. Commands it runs can't reach past the project, so bypassPermissions
is a reasonable choice inside it.
agent = Agent(llm=haiku, project_root=str(project), tools=[bash], permission_mode="bypassPermissions",
prompt="You work in this project with bash. Be brief.")
result = agent.run("Run the tests, then try to save a note to ~/notes.txt, and tell me what happened.")
for r in result.tool_results:
print(f"$ {r.output.strip().splitlines()[-1][:90] if r.output.strip() else ''}")
print("\n" + result.output[:500])$ exit=0 $ cat: ~/notes.txt: No such file or directory The tests passed: 1 test, exit code 0. pytest printed a warning that it couldn't write its cache directory (`.pytest_cache`), with "Operation not permitted". That didn't affect the result. The note was not saved. Writing to `~/notes.txt` failed with `Operation not permitted`, and the file doesn't exist. Both failures look like the sandbox blocking writes outside the project, which is consistent with the cache error. I didn't try another route around the restriction. If you want the note saved,
agent = Agent.with_builtins(llm=gemma, project_root=str(project), permissions=engine)
result = agent.run("Run the tests with pytest -q, then push to origin main.")
for r in result.tool_results:
print(f"{r.name:6} {r.output.strip()[:90]}")
print("\n" + result.output[:400])The request to push to the origin main branch was declined by the system security rules. I can still run the tests for you if you'd like.
shutil.rmtree(project, ignore_errors=True)PermissionEngine(allow, deny, ask) rules plus a mode decide every call; check() tests a policy offline.plan mode only reads; dontAsk refuses instead of asking.permission_callback decides in code; ApprovalQueue parks calls that can wait (await_decision = False).AgentHooks observe every call; a hook that raises stops the run.SandboxPolicy confines commands to the project, with no network, at the OS level.Next: Guide 10 — sub-agents and the verifier.