feat(analyst): add sandboxed python_exec tool by anandgupta42 · Pull Request #1538 · AltimateAI/altimate-code

anandgupta42 · 2026-10-17T06:27:48Z

Note: the database first-open race fix in this PR (setup-lock.ts and related files) is also proposed separately as #1541 and will drop out of this PR once that merges.

Issue for this PR

Related to #1537 (no Closes needed for a feat: title).

Type of change

Bug fix
New feature
Refactor / code improvement
Documentation

What does this PR do?

Why. The analyst agent denies bash, so it has no general-purpose compute. Parsing, statistics, row-wise text logic and cross-table work that SQL expresses badly have no path today.

What changed. Adds an analyst-only python_exec tool (new module-scope files src/altimate/tools/python-exec.ts and src/altimate/tools/python-sandbox.ts; no new members in any export namespace). Edits in upstream-shared files (agent/agent.ts, tool/registry.ts) are wrapped in altimate_change markers.

Security model:

Inputs are scratch tables exported to Parquet; save(df, name) writes DataFrames back to scratch only after a successful call. Python never gets warehouse connections.
The child runs with a minimal, explicit environment (PATH, HOME, TMPDIR, locale, a few thread limits). No inherited credentials, tokens or connection strings.
Persistent, size-capped, session-private workspace under the session's scratch directory; table names are restricted to plain identifiers (no path separators or schema prefixes); symlinks in the workspace are rejected; exceeding the cap kills the call and clears the workspace.
Memory limit (address space, with an RSS watchdog fallback where the OS refuses setrlimit), a clamped wall-clock deadline, process-group kill on timeout/abort. No hang on inherited pipes: the call returns on process exit or at the deadline, kills the process group and every tracked descendant (including ones started with start_new_session=True), then closes the pipes itself, so a descendant holding stdout open cannot block the result.
Filesystem confinement, fail-closed. Python may read only the session's Python directory (workspace and per-call files), the interpreter installation (sys.prefix, sys.base_prefix, exec prefixes, stdlib, site.getsitepackages(), sysconfig paths, and directories of native libraries it loads) and the minimal system files an interpreter needs. It may write only the session's Python directory. Subprocesses inherit the same confinement. An installation path that would expose / or the home directory is refused.
- macOS: sandbox-exec profile that denies file reads and writes outside the allowlist, all network, Apple Events, and Mach services outside a small allowlist (so LaunchServices cannot start unconfined helpers). Path metadata is allowed only on ancestors of allowlisted paths.
- Linux: bwrap with --unshare-all (network, PID, IPC, user, UTS and cgroup namespaces), --die-with-parent, --new-session, --cap-drop ALL, a fresh /tmp, /dev and /proc, read-only binds of exactly the allowlist (no host-root or home bind), merged-usr symlinks (/bin, /lib64, ...) recreated as symlinks, and a writable bind of the session directory. If bwrap is missing or cannot create namespaces, the tool refuses with a clear message. Landlock alone is not used as a fallback: it does not mediate connect() to pathname Unix sockets (Docker, D-Bus, SSH agent), which can reach host files.
- Signal isolation (macOS): the profile adds (deny signal) with (allow signal (target self) (target children)), so sandboxed code cannot signal the agent (os.kill(os.getppid(), ...)) or any other host process; it can still manage its own children. Verified on macOS with a test. On Linux the PID namespace already provides this.
- Stock Ubuntu 24.04: kernel.apparmor_restrict_unprivileged_userns=1 makes unprivileged bwrap fail (loopback: Failed RTM_NEWADDR), so python_exec refuses, which is intended. The refusal now names the AppArmor setting and the remedies (an AppArmor profile for bwrap, or the sysctl, as an administrator's choice), or says to install bubblewrap when it is missing. System settings are never changed automatically.
- Windows and other platforms: refused; no supported mechanism.
- Every mechanism must pass a self-test before first use: the sandboxed interpreter must import pandas and duckdb and read its own directory, while both Python and a cat subprocess fail to read a canary file outside the allowlist. A mechanism that fails is never used; if none passes, the tool refuses. Python is never run unconfined.
- Every result reports the mechanism, e.g. Isolation: filesystem bwrap (...); network isolated.
- Known residual on macOS: Seatbelt cannot block the KERN_PROCARGS2 sysctl, so sandboxed code can still read the arguments and environment of other processes owned by the same user (checked locally with several profile rules; none blocked it). It cannot read files, use the network or start unconfined helpers. The listing of / itself is readable because the dynamic loader needs it. On Linux the PID namespace hides other processes.
Registered only for analyst, and only when a Python with pandas and duckdb is found. MCP, plugin and file tools cannot claim the python_exec id. Bash remains denied for the analyst.

Before: the analyst can only use SQL tools. After: the analyst can materialize data to scratch, run Python over it, and read the saved tables back with SQL.

Flag: ALTIMATE_PYTHON_EXEC=0 disables the tool (it is not registered and calls are refused). ALTIMATE_PYTHON selects the interpreter.

How did you verify your code works?

Independent review of this revision (head 5115857): local Codex CLI could not run (usage limit), so a Sonnet agent reviewed it instead. Its findings were fixed: merged-usr hosts would have made bwrap unusable (symlinks are now recreated), Landlock fallback could reach host services over pathname Unix sockets (removed; Linux refuses without bwrap), the cat self-test leg lacked a positive control (added), and refusals were cached until restart (no longer). It also reported that a Seatbelt sysctl-read rule blocks KERN_PROCARGS2. I could not reproduce that here, so it is listed as a residual above. Earlier review (head da0beea) findings on host file reach are addressed by this revision.
bun test test/altimate/tools/python-exec.test.ts test/agent/python-exec.test.ts test/altimate/tools/tool-schema-anthropic.test.ts test/mcp/lifecycle.test.ts: 91 pass, 0 fail (macOS). test/agent alone: 163 pass; test/tool/registry.test.ts: 14 pass. New coverage: reads of a temp file in another directory, ~/.ssh, /etc/hosts, /etc/hostname and the home directory are denied; cat and /bin/sh subprocesses cannot read outside the allowlist but can read the workspace; pandas/duckdb Parquet round trip inside the sandbox; writes outside the workspace denied; the tool refuses when detection reports no mechanism; Windows/other platforms and Linux without a mechanism are refused; a fake bwrap that runs Python unconfined fails the self-test; exact bwrap argv (allowlist ro-binds, merged-usr symlinks, writable session bind, no host-root bind); macOS profile rules; allowlist rejection of / and home roots; MCP tools cannot claim python_exec.
Concurrent first run (database is locked). Starting 3 run --agent analyst processes at once against a fresh data directory failed one or two of them with database is locked (reproduced with ALTIMATE_PYTHON_EXEC=0 too, so it was a latent race that this tool's slower startup exposed, not a python_exec lock). Cause: the core SQLite opener ran PRAGMA journal_mode = WAL before any busy handler existed, and the legacy and core database layers both ran migrations whose deferred read-to-write upgrade fails at once with SQLITE_BUSY. Fix (head 01379b7): busy handler installed before the WAL switch, and first-run setup serialized across processes by an exclusive transaction on a sentinel database (packages/core/src/database/setup-lock.ts). Python discovery and the self-test never run inside any database transaction. New test/storage/concurrent-open.test.ts opens both layers from 4 simultaneous processes, 3 rounds; it fails on the previous head (database is locked) and passes now. Reproduction before/after: 3 concurrent CLI runs, 5 of 6 rounds failed at least one process before, 0 of 8 after. test/session 1302 pass; core database-migration 21 pass; typecheck clean.
Linux was not executed. These checks ran on macOS only. The bwrap path is covered by argv unit tests and by the fail-closed self-test that runs before first use on a real host; it has not run on a Linux machine yet.
bun run typecheck: clean.
bun run script/upstream/analyze.ts --markers --base origin/main --strict: reports no upstream-shared files for the main baseline (known v2 baseline limitation); markers were checked by hand.
Live check, CLI from source, analyst agent, google-vertex/gemini-3.8-flash, temp project with a 3-row DuckDB table. The Gemini enum-schema fix from fix: drop empty-string enum values from Gemini tool schemas #1532 is not on main, so I ran against a throwaway local branch with only that fix applied (not in this PR). The agent called sql_materialize (3 rows to scratch), one python_exec (saved wc), sql_execute on wc, then answered: total word count 9, correlation 0.99919, matching a hand calculation. The run reported network isolated and the RSS-watchdog memory fallback on macOS.
An earlier live run, before read confinement, showed the model using python_exec to read host files and run git. That is the gap this revision closes: host reads are now denied by the OS sandbox and the tool refuses where no sandbox can be enforced.

Screenshots / recordings

N/A (no UI change).

Checklist

I have tested my changes locally
I have not included unrelated changes in this PR

🤖 Generated with Claude Code

Summary by CodeRabbit

New Features
- The analyst can use Python for non-SQL calculations and cross-table analysis with data materialized in the session workspace. Availability depends on Python requirements and secure execution support; the tool is not available to other agents.
Security
- Python runs without network access and is restricted to approved files and the session workspace. Execution has time and memory limits, output is bounded, and workspace storage is capped. If secure confinement is unavailable, Python execution is refused.
- External tools named python_exec are excluded from tool discovery.
Bug Fixes
- Improved database reliability when multiple processes initialize or open the same database concurrently.

Note

High Risk
Introduces sandboxed arbitrary Python execution with complex OS confinement and process cleanup; misconfiguration or sandbox bypass would be security-critical, though the design is fail-closed and analyst-scoped.

Overview
Adds an analyst-only python_exec tool so read-only analysis can run Python (parsing, stats, row logic) after data is in session scratch tables—without bash or warehouse credentials.

Execution exports declared scratch inputs to Parquet, runs user code with altimate_io.load / save, and imports successful save outputs back to scratch. A session-private, size-capped workspace persists across calls; timeouts, memory limits, and process-group cleanup apply on abort or overrun.

OS confinement is mandatory: macOS sandbox-exec or Linux bwrap, with self-test before use; the tool refuses if no mechanism works (e.g. missing bwrap, AppArmor blocking user namespaces). The child gets a minimal env (no inherited secrets), no network, and restricted filesystem access.

Wiring: analyst permission and prompt mention python_exec; the tool registers only when pandas/duckdb Python is found (ALTIMATE_PYTHON_EXEC=0 disables). python_exec is reserved in the tool registry and MCP catalog like answer_commit. Tests cover sandbox behavior, registration scope, and MCP collision avoidance.

^{Reviewed by Cursor Bugbot for commit 35ef388. Bugbot is set up for automated code reviews on this repo. Configure here.}

The `analyst` agent denies bash, so it has no general-purpose compute for parsing, statistics or row-wise text logic. Add an analyst-only `python_exec` tool. - Inputs are scratch tables exported to Parquet; `save(df, name)` writes DataFrames back to scratch after a successful call. - The child gets a minimal environment (no credentials or connection strings) and never sees warehouse connections. - Persistent, size-capped, session-private workspace; memory and time limits; network isolation where the OS allows it (`unshare`, `sandbox-exec`). - Registered only for `analyst` when Python with pandas and duckdb is found; `ALTIMATE_PYTHON_EXEC=0` disables it. Bash stays denied. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

chatgpt-codex-connector · 2026-10-17T06:27:56Z

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📝 Walkthrough

This change adds an analyst-only python_exec tool that runs Python under detected OS confinement and exchanges data through scratch tables. It also adds cross-process locking around SQLite setup and WAL initialization.

Changes: Analyst Python Execution

Layer / File(s)	Summary
Confinement detection and enforcement `packages/opencode/src/altimate/tools/python-sandbox.ts`, `packages/opencode/test/altimate/tools/python-exec.test.ts`	The sandbox supports macOS `sandbox-exec` and Linux `bwrap`. It builds read and write rules and tests confinement with canaries. Tests cover platform rules and refusal when confinement does not pass.
Interpreter discovery and process controls `packages/opencode/src/altimate/tools/python-exec.ts`, `packages/opencode/test/altimate/tools/python-exec.test.ts`	The tool discovers Python with pandas and DuckDB. It applies process, timeout, memory, output, and workspace limits. Tests cover discovery, environment isolation, timeout bounds, output clipping, and descendant process identity.
Scratch data transfer and tool execution `packages/opencode/src/altimate/tools/python-exec.ts`, `packages/opencode/test/altimate/tools/python-exec.test.ts`	The tool exports scratch tables to Parquet, runs Python in the confined process, and imports output tables only after successful execution. Tests cover table transfer, workspace behavior, cancellation, and errors.
Analyst registration and reserved tool filtering `packages/opencode/src/agent/agent.ts`, `packages/opencode/src/altimate/prompts/analyst.txt`, `packages/opencode/src/tool/registry.ts`, `packages/opencode/src/mcp/index.ts`, `packages/opencode/test/agent/python-exec.test.ts`, `packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts`, `packages/opencode/test/mcp/lifecycle.test.ts`	The analyst permission rules and prompt include `python_exec`. The registry adds it only when enabled and available. Tests cover registration and reserved-name filtering.

SQLite Setup Locking

Layer / File(s)	Summary
Cross-process setup lock and database initialization `packages/core/src/database/setup-lock.ts`, `packages/core/src/database/database.ts`, `packages/core/src/database/sqlite..ts`, `packages/opencode/src/storage/db.ts`, `packages/opencode/test/storage/`	The shared setup lock serializes SQLite setup and WAL changes. Database initialization applies the busy timeout before WAL setup. A concurrent-open test starts multiple processes against the same data directory.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant Analyst
  participant PythonExecTool
  participant Scratch
  participant ConfinedPython
  Analyst->>PythonExecTool: Submit code and scratch table names
  PythonExecTool->>Scratch: Export requested tables to Parquet
  PythonExecTool->>ConfinedPython: Run code with session workspace
  ConfinedPython->>PythonExecTool: Return status and output tables
  PythonExecTool->>Scratch: Import output tables after successful execution
  PythonExecTool->>Analyst: Return execution result

Merge Risk: 🟡 Moderate · up to 01379

Concurrent database initialization can fail when legacy and core setup overlap. Resolve that race before merging, and confirm the Node lock timeout on supported runtimes.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 59.09% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 44 functions across 16 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks: 4 passed

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Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.
Description check		The description follows the required template. It identifies the related issue, marks the change as a new feature, explains the implementation and security model, documents verification results and li…
Title check		The title clearly and concisely identifies the main change: adding a sandboxed python_exec tool for the analyst agent.

Full details: Description check

Explanation

The description follows the required template. It identifies the related issue, marks the change as a new feature, explains the implementation and security model, documents verification results and limitations, notes that Linux was not tested, and completes the checklist. It also discloses the separate database setup-lock change.

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github-actions · 2026-10-17T06:28:21Z

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…n macOS Independent review found that the analyst's Python child could write anywhere the user can. On macOS the `sandbox-exec` profile now also denies `file-write*` outside the session's Python directory (plus null/tty devices). Reads and the Linux path are unchanged. The result text states which confinement applied, and a test covers the write denial. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

anandgupta42 · 2026-10-17T06:31:22Z

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kilo-code-bot · 2026-10-17T06:35:19Z

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (17 files)

packages/core/src/database/database.ts
packages/core/src/database/setup-lock.ts
packages/core/src/database/sqlite.bun.ts
packages/core/src/database/sqlite.node.ts
packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/storage/db.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts
packages/opencode/test/storage/concurrent-open.test.ts
packages/opencode/test/storage/fixture/open-database.ts

Previous Review Summaries (10 snapshots, latest commit ae84ca4)

Current summary above is authoritative. Previous snapshots are kept for context only.

Previous review (commit `ae84ca4`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (17 files)

packages/core/src/database/database.ts
packages/core/src/database/setup-lock.ts
packages/core/src/database/sqlite.bun.ts
packages/core/src/database/sqlite.node.ts
packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/storage/db.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts
packages/opencode/test/storage/concurrent-open.test.ts
packages/opencode/test/storage/fixture/open-database.ts

Previous review (commit `01379b7`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (17 files)

packages/core/src/database/database.ts
packages/core/src/database/setup-lock.ts
packages/core/src/database/sqlite.bun.ts
packages/core/src/database/sqlite.node.ts
packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/storage/db.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts
packages/opencode/test/storage/concurrent-open.test.ts
packages/opencode/test/storage/fixture/open-database.ts

Previous review (commit `c248e32`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `6fff449`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `0dc826a`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `87f416c`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `0d7df67`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `f7dc69d`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `5115857`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (10 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

Previous review (commit `54ab3df`)

Status: 2 Issues Found | Recommendation: Address before merge

Overview

Severity	Count
CRITICAL	0
WARNING	2
SUGGESTION	0

Issue Details (click to expand)

WARNING

File	Line	Issue
`packages/opencode/src/tool/registry.ts`	68	Nested `altimate_change` marker inside an already-marked block
`packages/opencode/src/tool/registry.ts`	550	`python_exec` is reserved from file/plugin tools here, but not from MCP tools in `packages/opencode/src/mcp/index.ts`

Files Reviewed (7 files)

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/tool/registry.ts - 2 issues
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts

Fix these issues in Kilo Cloud

_{Reviewed by gemini-4-argon · Input: 94.2K · Output: 1.2K · Cached: 286.1K}

_{Review guidance: REVIEW.md from base branch main}

…andbox Analyst Python could read any host file and spawn unconfined subprocesses; on Linux nothing was confined. `python_exec` now runs only under an enforced OS sandbox and refuses otherwise. - New `python-sandbox.ts`: read allowlist built from the interpreter (`sys.prefix`, base/exec prefixes, stdlib, `site.getsitepackages()`, `sysconfig` paths, directories of loaded native libraries) plus minimal system paths; roots exposing `/` or the home directory are refused. - macOS: `sandbox-exec` profile denies file reads and writes outside the allowlist, network, Apple Events and Mach services outside a small list. - Linux: `bwrap` with `--unshare-all`, `--die-with-parent`, `--new-session`, `--cap-drop ALL`, fresh `/tmp`, `/dev`, `/proc`, read-only binds of the allowlist, merged-usr symlinks, and a writable bind of the session dir. Without a working `bwrap` the tool refuses (Landlock alone does not mediate pathname Unix socket connects). - Windows and other platforms: refused. - Each mechanism must pass a self-test before use: Python and a `cat` subprocess fail to read a canary outside the allowlist, while reading inside works. Refusals are not cached. - Results report `filesystem <mechanism>` and `network isolated`. - Interpreter discovery and detection no longer block the event loop. - Reserve `python_exec` from MCP tools; drop nested registry markers. - Tests: host-file and subprocess read denial, pandas/duckdb round trip, refusal when detection fails, fake sandbox rejected by the self-test, exact bwrap argv, macOS profile, allowlist rules, MCP reservation. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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Inline comments:
Review comments at @packages/opencode/src/altimate/tools/python-exec.ts:
- Around line 252-295: Update the process completion handling in the run flow so
it does not rely solely on the child’s close event, which can wait indefinitely
for descendant-held stdout or stderr pipes. On exit, kill remaining descendants
and schedule pipe destruction followed by resolution after a short grace period;
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Review comments at @packages/opencode/src/altimate/tools/python-sandbox.ts:
- Around line 221-230: Update the macOS Seatbelt profile returned by this
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Review comments at @packages/opencode/test/altimate/tools/python-exec.test.ts:
- Around line 46-47: Split the Python-only `e2e` gate from sandbox-dependent
coverage: call `confinementFor(python)` once at module load and add a `confined`
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📥 Commits

Reviewing files that changed from the base of the PR and between 19f909c and 5115857.

📒 Files selected for processing: 10

packages/opencode/src/agent/agent.ts
packages/opencode/src/altimate/prompts/analyst.txt
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/mcp/index.ts
packages/opencode/src/tool/registry.ts
packages/opencode/test/agent/python-exec.test.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
packages/opencode/test/altimate/tools/tool-schema-anthropic.test.ts
packages/opencode/test/mcp/lifecycle.test.ts

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…s, explain Linux refusals - `run` resolves on process `exit` or timeout, kills the process group plus every recorded descendant (including `start_new_session` ones), then closes the pipes, so a descendant that holds stdout open can no longer hang the call. - macOS profile denies `signal` except to the process itself and its children, so sandboxed code cannot signal the agent or other host processes. - Linux refusal names the missing `bubblewrap` package, or the AppArmor `kernel.apparmor_restrict_unprivileged_userns=1` restriction and its admin remedies. - Tests that need a working sandbox skip with a reason when none exists; a dedicated test asserts refusal in that case. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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anandgupta42 · 2026-10-17T15:10:18Z

@codex review

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Inline comments:
Review comments at @packages/core/src/database/setup-lock.ts:
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Review comments at @packages/core/src/database/sqlite.node.ts:
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packages/core/src/database/database.ts
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packages/core/src/database/sqlite.bun.ts
packages/core/src/database/sqlite.node.ts
packages/opencode/src/altimate/tools/python-exec.ts
packages/opencode/src/altimate/tools/python-sandbox.ts
packages/opencode/src/storage/db.ts
packages/opencode/test/altimate/tools/python-exec.test.ts
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Wraps the setup-lock import, the reworked `layer` and `layerFromPath` in a single `altimate_change` upstream_fix block so Marker Guard passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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# Conflicts: # packages/opencode/src/altimate/prompts/analyst.txt # packages/opencode/src/tool/registry.ts

anandgupta42 · 2026-10-17T18:34:14Z

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…ils closed on host environment exposure - macOS profile: `(deny process-fork)` blocks fork, posix_spawn, `subprocess` and `multiprocessing`, so a double-forked `setsid` grandchild can no longer escape cleanup; `(deny process-info*)` + `(allow process-info* (target self))` blocks proc_info inspection of other processes; signals limited to self. - Seatbelt does not mediate the `KERN_PROCARGS2` sysctl (verified on macOS 26.5: `(deny sysctl*)`, name filters, `process-info*` and deny-default all still return same-user process environments). Blocking `ctypes` is not an option because pandas imports it. The self-test now starts a host canary process with a marker in its environment and refuses any mechanism under which sandboxed Python can read it, so macOS currently refuses `python_exec` with that reason. - Self-test on macOS also requires every child-process attempt to fail; on Linux it keeps the subprocess canary check (bwrap already uses `--unshare-all` and `--die-with-parent`). - Tool description notes that child processes are blocked on macOS. - Tests: profile-level sandbox-exec regressions (fork/spawn denial with no surviving grandchild, pandas/NumPy/DuckDB still work, readable host environment forces refusal), self-test fails closed when fork denial is stripped, tool-level host-environment and double-fork checks; subprocess tests are now bwrap-only. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… passes - `pythonExecAvailable()` now also requires `confinementFor(python)` to succeed, so hosts whose sandbox self-test refuses (currently macOS, where `KERN_PROCARGS2` exposes host environments) never see the tool. - The verdict, including a refusal, is cached per interpreter and process; the refusal reason is logged once at debug level. `resetConfinement()` clears it. - Registry gate simplified inside its existing `altimate_change` block. - Tests: the analyst catalogue omits `python_exec` when an injected self-test refuses and includes it when it passes, without rerunning the self-test on a second build; discovery test expects availability to follow the self-test. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

anandgupta42 · 2026-10-17T19:28:07Z

Parked as draft (owner decision pending; not closed).

No measured accuracy benefit from this tool in our evaluation so far.
macOS: sandbox-exec cannot block the process-arguments sysctl, so sandboxed Python could read other same-user processes' environments. The tool is now registered only when the OS sandbox self-test passes (6c34ba9), which hides it on macOS; child processes are denied there (b9f6ccf).
Linux (bwrap) path is unchanged and still fail-closed.

Revive only with a stronger isolation layer for macOS (separate user or VM) and a demonstrated benefit.

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chore: mark the first-run setup changes in the shared database layer

ae84ca4

Wraps the setup-lock import, the reworked `layer` and `layerFromPath` in a single `altimate_change` upstream_fix block so Marker Guard passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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chore: sync the shared database first-open fix with #1541

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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/main' into feat/analyst-python-exec

35ef388

# Conflicts: # packages/opencode/src/altimate/prompts/analyst.txt # packages/opencode/src/tool/registry.ts

anandgupta42 and others added 2 commits October 17, 2026 12:08

anandgupta42 marked this pull request as draft October 17, 2026 19:28

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chatgpt-codex-connector Bot commented Oct 17, 2026 •

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kilo-code-bot Bot commented Oct 17, 2026 •

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