Add Pyodide sandbox code interpreter MCP server

[Ali Keramati (alikera)]

Adds a pyodide-based code interpreter, originally written by Susana Palmaz (@susana-palmaz): code_interpreter, list_sandbox_files and search_sandbox_files.

Security

Pyodide isn't an isolation boundary. Agent code can reach the Node host: host files, process execution, env vars. docs/sandbox_code_interpreter.md sets out the threat model.

code_interpreter now refuses to run unless THINKINGBOX_SANDBOX_ALLOW_UNCONFINED=1 is set by whatever launches the server. It's deliberately not in servers.yaml, so the unsafe mode isn't the default. The file tools still work without it.

Trusted code only, and no secrets in that environment. Real confinement needs a container and isn't in this PR.

Testing

gpt-4o ran the revenue test end to end and passed: it wrote pandas against a CSV in the workspace, carried the DataFrame across two calls, and got every regional total right to the cent.

Separately drove the tool directly against support/tau_bench/airline_data (5.2 MB of flights, reservations and users). Aggregations matched host CPython exactly, and a file rewritten from inside the session came back byte-identical. Also round-tripped the document and plotting libraries it advertises.

CI: 152 passed, 2 skipped, 6 xfailed. The xfails probe the escapes above and should start passing once the worker is confined.

Fixed while porting

• Output over 64 KB broke the worker (asyncio's default line limit); a mid-sized DataFrame hits it
• Malformed frames desynced the stream, so the next call returned the previous call's result
• search_sandbox_files crashed on patterns like '', ***, /etc/passwd
• Vendored wheels weren't checked against PyPI's sha256

[Copilot]

Pull request overview

Ports a Pyodide-based sandbox/code-interpreter MCP server into this repo, including a Node.js worker that hosts Pyodide, Python-side orchestration via FastMCP, workspace copy-on-write isolation, and a full integration test suite/documentation.

Changes:

• Adds a new sandbox MCP server (mcp_sandbox.py) backed by a long-lived Node/Pyodide worker with a JSON-over-stdio protocol.
• Implements workspace file listing/search tools plus copy-on-write isolation via NODEFS hooks and a per-session seeded workspace copy.
• Introduces Node worker packaging/CI wiring (npm install, vendored wheels postinstall) and extensive pytest coverage + docs.

Reviewed changes

Copilot reviewed 13 out of 15 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/scripts/download-wheels.mjs	NPM postinstall script to vendor pure-Python wheels from PyPI into wheels/.
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/sandbox.py	Host-side workspace file listing/search helpers with traversal protections.
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/pypi-packages.mjs	Declares PyPI-only packages to preinstall via micropip (vendored when possible).
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/pyodide_worker.mjs	Node worker: loads Pyodide, installs packages, mounts /workspace, applies COW protections, executes code.
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/package.json	Declares pyodide dependency and postinstall wheel-vendoring hook.
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/package-lock.json	Locks Node dependencies for the worker.
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/code_interpreter.py	Python supervisor for the Node worker (spawn, handshake, timeouts, serialization, effects log).
servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/init.py	Ensures setuptools package discovery of the sandbox subpackage.
servers/thinkingbox_tools/thinkingbox_tools/mcp_sandbox.py	FastMCP server defining sandbox tools + session lifecycle and workspace seeding.
servers/thinkingbox_tools/tests/test_sandbox_server.py	Integration tests for tool discovery, file ops, isolation/COW behavior, and interpreter semantics.
servers/thinkingbox_tools/pyproject.toml	Packages sandbox worker assets as Python package data.
servers/servers.yaml	Registers the new sandbox server entry.
docs/sandbox_code_interpreter.md	Architecture/design documentation and operational guidance for the sandbox server.
.gitignore	Ignores node_modules/ for the new Node worker.
.github/workflows/test-thinkingbox-tools.yml	Adds Node setup + npm ci for the sandbox worker prior to pytest.

Files not reviewed (1)

• servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/package-lock.json: Generated file

Suppressed comments (1)

servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/scripts/download-wheels.mjs:56

• This wheel download fetch() also has no timeout, so a stuck transfer can hang npm install/npm ci. Adding a timeout here keeps postinstall bounded and matches the intended “best-effort vendoring” behavior.

    console.log(`[download-wheels] Downloading: ${wheel.filename}`);
    const wRes = await fetch(wheel.url);
    if (!wRes.ok) {
        console.warn(`[download-wheels] Download failed (${wRes.status}) for ${wheel.url} — skipping`);
        return;
    }
    await writeFile(dest, Buffer.from(await wRes.arrayBuffer()));

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[Ali Keramati (alikera)]

@microsoft-github-policy-service agree company="Microsoft"

…

On Wed, Aug 26, 2026 at 6:35 PM microsoft-github-policy-service[bot] < ***@***.***> wrote: *microsoft-github-policy-service[bot]* left a comment (microsoft/thinkingbox-data#22) <#22 (comment)> Ali Keramati ***@***.***) <https://github.com/alikera> please read the following Contributor License Agreement(CLA). If you agree with the CLA, please reply with the following information. @microsoft-github-policy-service agree [company="{your company}"] Options: - (default - no company specified) I have sole ownership of intellectual property rights to my Submissions and I am not making Submissions in the course of work for my employer. @microsoft-github-policy-service agree - (when company given) I am making Submissions in the course of work for my employer (or my employer has intellectual property rights in my Submissions by contract or applicable law). I have permission from my employer to make Submissions and enter into this Agreement on behalf of my employer. By signing below, the defined term “You” includes me and my employer. @microsoft-github-policy-service agree company="Microsoft" Contributor License Agreement Contribution License Agreement This Contribution License Agreement (*“Agreement”*) is agreed to by the party signing below (*“You”*), and conveys certain license rights to Microsoft Corporation and its affiliates (“Microsoft”) for Your contributions to Microsoft open source projects. This Agreement is effective as of the latest signature date below. 1. *Definitions*. *“Code”* means the computer software code, whether in human-readable or machine-executable form, that is delivered by You to Microsoft under this Agreement. *“Project”* means any of the projects owned or managed by Microsoft and offered under a license approved by the Open Source Initiative (www.opensource.org). *“Submit”* is the act of uploading, submitting, transmitting, or distributing code or other content to any Project, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Project for the purpose of discussing and improving that Project, but excluding communication that is conspicuously marked or otherwise designated in writing by You as “Not a Submission.” *“Submission”* means the Code and any other copyrightable material Submitted by You, including any associated comments and documentation. 2. *Your Submission*. You must agree to the terms of this Agreement before making a Submission to any Project. This Agreement covers any and all Submissions that You, now or in the future (except as described in Section 4 below), Submit to any Project. 3. *Originality of Work*. You represent that each of Your Submissions is entirely Your original work. Should You wish to Submit materials that are not Your original work, You may Submit them separately to the Project if You (a) retain all copyright and license information that was in the materials as You received them, (b) in the description accompanying Your Submission, include the phrase “Submission containing materials of a third party:” followed by the names of the third party and any licenses or other restrictions of which You are aware, and (c) follow any other instructions in the Project’s written guidelines concerning Submissions. 4. *Your Employer*. References to “employer” in this Agreement include Your employer or anyone else for whom You are acting in making Your Submission, e.g. as a contractor, vendor, or agent. If Your Submission is made in the course of Your work for an employer or Your employer has intellectual property rights in Your Submission by contract or applicable law, You must secure permission from Your employer to make the Submission before signing this Agreement. In that case, the term “You” in this Agreement will refer to You and the employer collectively. If You change employers in the future and desire to Submit additional Submissions for the new employer, then You agree to sign a new Agreement and secure permission from the new employer before Submitting those Submissions. 5. *Licenses*. - *Copyright License*. You grant Microsoft, and those who receive the Submission directly or indirectly from Microsoft, a perpetual, worldwide, non-exclusive, royalty-free, irrevocable license in the Submission to reproduce, prepare derivative works of, publicly display, publicly perform, and distribute the Submission and such derivative works, and to sublicense any or all of the foregoing rights to third parties. - *Patent License*. You grant Microsoft, and those who receive the Submission directly or indirectly from Microsoft, a perpetual, worldwide, non-exclusive, royalty-free, irrevocable license under Your patent claims that are necessarily infringed by the Submission or the combination of the Submission with the Project to which it was Submitted to make, have made, use, offer to sell, sell and import or otherwise dispose of the Submission alone or with the Project. - *Other Rights Reserved*. Each party reserves all rights not expressly granted in this Agreement. No additional licenses or rights whatsoever (including, without limitation, any implied licenses) are granted by implication, exhaustion, estoppel or otherwise. 6. *Representations and Warranties*. You represent that You are legally entitled to grant the above licenses. You represent that each of Your Submissions is entirely Your original work (except as You may have disclosed under Section 3). You represent that You have secured permission from Your employer to make the Submission in cases where Your Submission is made in the course of Your work for Your employer or Your employer has intellectual property rights in Your Submission by contract or applicable law. If You are signing this Agreement on behalf of Your employer, You represent and warrant that You have the necessary authority to bind the listed employer to the obligations contained in this Agreement. You are not expected to provide support for Your Submission, unless You choose to do so. UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING, AND EXCEPT FOR THE WARRANTIES EXPRESSLY STATED IN SECTIONS 3, 4, AND 6, THE SUBMISSION PROVIDED UNDER THIS AGREEMENT IS PROVIDED WITHOUT WARRANTY OF ANY KIND, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY OF NONINFRINGEMENT, MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. 7. *Notice to Microsoft*. You agree to notify Microsoft in writing of any facts or circumstances of which You later become aware that would make Your representations in this Agreement inaccurate in any respect. 8. *Information about Submissions*. You agree that contributions to Projects and information about contributions may be maintained indefinitely and disclosed publicly, including Your name and other information that You submit with Your Submission. 9. *Governing Law/Jurisdiction*. This Agreement is governed by the laws of the State of Washington, and the parties consent to exclusive jurisdiction and venue in the federal courts sitting in King County, Washington, unless no federal subject matter jurisdiction exists, in which case the parties consent to exclusive jurisdiction and venue in the Superior Court of King County, Washington. The parties waive all defenses of lack of personal jurisdiction and forum non-conveniens. 10. *Entire Agreement/Assignment*. This Agreement is the entire agreement between the parties, and supersedes any and all prior agreements, understandings or communications, written or oral, between the parties relating to the subject matter hereof. This Agreement may be assigned by Microsoft. — Reply to this email directly, view it on GitHub <#22?email_source=notifications&email_token=AWEMZKF4MCZJBFZUQ26JMFL5L6F55A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNBTGMZDGNJRGU32M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5433235157>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWEMZKGCZX7UMPEAFHAZ77D5L6F55AVCNFSNUABGKJSXA33TNF2G64TZHMYTEMJYGMZTGNRVGU5US43TOVSTWNJSGYZDSOBTGI2DNILWAI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[github-actions]

⚠️ Deprecation Warning: The deny-licenses option is deprecated for possible removal in the next major release. For more information, see issue 997.

Dependency Review

The following issues were found:

• ❌ 1 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 1 package(s) with unknown licenses.

See the Details below.

Vulnerabilities

servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/package-lock.json

Name	Version	Vulnerability	Severity
ws	8.19.0	ws: Memory exhaustion DoS from tiny fragments and data chunks	high

Only included vulnerabilities with severity high or higher.

License Issues

.github/workflows/test-thinkingbox-tools.yml

Package	Version	License	Issue Type
actions/setup-node	7.*.*	Null	Unknown License

Denied Licenses:

GPL-2.0, GPL-3.0, AGPL-3.0

OpenSSF Scorecard

Package	Version	Score	Details
actions/actions/setup-node	7.*.*	🟢 6.4	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 21 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Binary-Artifacts 🟢 9 binaries present in source code Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies 🟢 5 dependency not pinned by hash detected -- score normalized to 5 License 🟢 10 license file detected Fuzzing ⚠️ 0 project is not fuzzed Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 9 security policy file detected Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches SAST 🟢 10 SAST tool is run on all commits
npm/ws	8.19.0	🟢 5.5	Details Check Score Reason Packaging ⚠️ -1 packaging workflow not detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege Code-Review ⚠️ 0 Found 1/29 approved changesets -- score normalized to 0 Maintained 🟢 10 18 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10 Binary-Artifacts 🟢 10 no binaries found in the repo Security-Policy 🟢 10 security policy file detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches Signed-Releases ⚠️ -1 no releases found SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
npm/@types/emscripten	1.41.5	🟢 6.6	Details Check Score Reason Code-Review 🟢 9 Found 29/30 approved changesets -- score normalized to 9 Packaging ⚠️ -1 packaging workflow not detected CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Maintained 🟢 10 30 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Security-Policy 🟢 10 security policy file detected License 🟢 9 license file detected Signed-Releases ⚠️ -1 no releases found Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0 Pinned-Dependencies 🟢 8 dependency not pinned by hash detected -- score normalized to 8 Binary-Artifacts 🟢 10 no binaries found in the repo Fuzzing ⚠️ 0 project is not fuzzed
npm/pyodide	0.29.4	🟢 5.6	Details Check Score Reason Maintained 🟢 10 30 commit(s) and 22 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Code-Review ⚠️ 2 Found 6/24 approved changesets -- score normalized to 2 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Security-Policy ⚠️ 0 security policy file not detected License 🟢 10 license file detected Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Binary-Artifacts 🟢 7 binaries present in source code Packaging 🟢 10 packaging workflow detected Fuzzing ⚠️ 0 project is not fuzzed SAST 🟢 3 SAST tool is not run on all commits -- score normalized to 3 Pinned-Dependencies 🟢 6 dependency not pinned by hash detected -- score normalized to 6

Scanned Files

• .github/workflows/test-thinkingbox-tools.yml
• servers/thinkingbox_tools/thinkingbox_tools/toolslib/sandbox/package-lock.json

[Ali Keramati (alikera)]

Security review: the Pyodide worker is not an isolation boundary

I audited the escape vectors raised in review. They reproduce. Posting findings and a proposed design before making broad changes, as requested.

Audit results

Measured against the pyodide@0.29.4 install this PR pins, loading Pyodide exactly as pyodide_worker.mjs does. Each probe measured reachability only — nothing destructive was executed, and the file-read probe used a sentinel file the audit created itself, not a real system file.

Capability	Result
import js → js.process	reachable (JsProxy)
pyodide_js._api exposed to Python	reachable
_api.loadBinaryFile exposed	reachable
Host file read outside session dir via _api.loadBinaryFile	READ_OK
JsProxy.constructor.constructor (Function ctor)	reachable
process visible via Function ctor	process-visible
process.env readable	76 variables
node:fs via dynamic import()	FS_MODULE_OK
node:child_process via dynamic import()	CHILD_PROCESS_OK

So agent-supplied Python has host filesystem read/write, process execution, and full environment-variable access. The NODEFS copy-on-write layer is irrelevant to this: it guards /workspace, and these vectors bypass /workspace entirely.

This is consistent with Pyodide's own documented position — it provides memory safety via WASM, but deliberately exposes a Python↔JS FFI and is explicitly not a security sandbox for untrusted code.

The documentation is currently wrong

docs/sandbox_code_interpreter.md states:

The WASM runtime is the trust boundary: user code cannot reach the host filesystem, network, or processes except through the FS bridges we explicitly expose.

That is false as written, and it's the most dangerous thing in this PR — it would lead a reader to route untrusted input here. I'm correcting the threat model in this PR regardless of what we decide about isolation.

Why in-process hardening cannot fix this

Worth stating explicitly, because these are the obvious first attempts:

• jsglobals: {} — does not help. Function bodies are evaluated in the global scope, not the restricted object. Any reachable JS function gives .constructor.constructor, and Function("return process")() returns the real process regardless.
• Deleting/unregistering modules — does not help. Pyodide's internals capture live JsProxy references at load time; those survive later deletion of the module bindings.
• Node's permission model (--permission) — useful defense-in-depth, insufficient alone. It is still experimental, does not gate process.env reads, and is not a substitute for an OS boundary.

The common failure is that all three try to remove names while leaving live references reachable inside the same process and privilege domain.

Proposed design: move the boundary to the OS

Run the worker under an owner-approved OS/container boundary, so escaping Pyodide only lands the attacker in an already-empty jail.

Preferred — containerized worker:

• --network=none (no network)
• read-only root filesystem; --tmpfs /tmp
• only the session directory bind-mounted read-write; no other host path
• --cap-drop=ALL, --security-opt=no-new-privileges, non-root user
• explicitly empty environment (no inherited secrets) — currently 76 vars are visible
• --pids-limit, memory and CPU limits (also gives us a real answer for runaway code, which today only has a wall-clock timeout)

Fallback where a container runtime is unavailable: fail closed. CodeInterpreter._start() should refuse to launch and return a clear error rather than silently running unconfined, with an explicit opt-out env var for trusted local development.

Defense-in-depth (not load-bearing): Node permission flags, dropping _api bindings, jsglobals restriction.

Affected files if we proceed

File	Change
toolslib/sandbox/code_interpreter.py	spawn via container runtime; fail closed when absent
toolslib/sandbox/sandbox.Dockerfile	new — pinned Node + pyodide + vendored wheels
mcp_sandbox.py	session-dir mount wiring
pyodide_worker.mjs	defense-in-depth hardening
.github/workflows/test-thinkingbox-tools.yml	build/pull image before tests
tests/test_sandbox_isolation.py	new — capability regression tests
docs/sandbox_code_interpreter.md	threat model rewrite

That is a rewrite of the execution model and a CI-shape change, so I am not doing it unilaterally in this port. It needs an owner decision on runtime (Docker vs Podman vs rootless), base image, and whether eval throughput can absorb per-session container startup.

What I am changing in this PR now (bounded)

1. Correct the threat model in the docs and the code_interpreter tool description — remove the false "cannot reach the host" claims, state plainly that this is not a security boundary and must only run trusted//first-party agent code until isolation lands.
2. Fix the workspace link issue — reject symlinks/junctions/reparse points whose target escapes workspace_dir; materialize in-workspace links as real copies.
3. Add regression tests — link-handling tests that fail against the unfixed code, plus capability tests marked xfail(strict=True) so they are recorded as known-broken and will fail loudly the moment isolation makes them pass, forcing the marker to be removed.

Keeping this as a draft.

[Ali Keramati (alikera)]

Note on the Dependency Review "unknown license" notice

The Dependency Review bot comment on this PR flags:

We could not detect a license for the following dependencies:
.github/workflows/test-thinkingbox-tools.yml » actions/setup-node@7.*.*

This is a false positive and is not failing the check. actions/setup-node is MIT-licensed (GitHub's own license API returns spdx_id: MIT with a LICENSE file present). The action cannot resolve licenses for GitHub Actions referenced by floating major tag, so it reports "unknown" rather than "missing".

From the same run:

• Vulnerabilities — did not detect any vulnerable packages with severity level "high" or higher
• Denied — did not detect any denied packages
• The gate is deny-licenses: GPL-2.0, GPL-3.0, AGPL-3.0; unknown is not denied
• The review check reports pass

I deliberately did not silence it by pinning to a commit SHA. Every action in this repo uses a floating major tag — actions/checkout@v7, setup-python@v7, setup-uv@v7, codeql-action/*@v4, dependency-review-action@v5 — so setup-node@v7 follows the existing convention, and this notice would appear for any action added to any workflow here. If SHA-pinning is wanted, it should be done for all actions in a separate PR rather than for one action in this one.

Separately, the same bot comment carries a deprecation warning for the deny-licenses option. That lives in .github/workflows/dep-review.yml, which this PR does not touch — worth tracking separately.

Current status on fbd09bb: all six checks pass with zero annotations, no open code-scanning alerts, and no unresolved review threads. CodeQL reports "No new alerts in code changed by this pull request."

[Ali Keramati (alikera)]

One thing worth deciding before this merges: the interpreter refusing to start without THINKINGBOX_SANDBOX_ALLOW_UNCONFINED=1 wasn't part of the original ask, and it does mean eval runs need that variable exported.

Happy to drop it (one commit) and keep just the port, the bug fixes, and the docs correction, if the lighter version is preferred.

[Susana Palmaz (susana-palmaz)]

We have moved away from pyodide and into using python WASM instead. Security and speed were the main concerns and we wanted to only support one backend. There are some downsides to the change, related to support for not pure cython based dependencies, but we can live with that. I don't think pyodide it should be re-introduced, but I would welcome a thorough review like the one done here for python wasm.
See merged PR where pyodide was removed: https://github.com/microsoft/AI.ThinkingBox.Data/pull/224