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Snakemake: GitPython: Newline injection in config_writer().set_value() enables RCE via core.hooksPath (CVE-2026-44244)

0
High
Published: 08/13/2026 (08/13/2026, 17:34:42 UTC)
Source: GCVE Database
Product: snakemake

Description

`GitConfigParser.set_value()` passes values to Python's `configparser` without validating for newlines. GitPython's own `_write()` converts embedded newlines into indented continuation lines (e.g. `\n` becomes `\n\t`), but Git still accepts an indented `[core]` stanza as a section header — so the injected `core.hooksPath` becomes effective configuration. Any Git operation that invokes hooks (commit, merge, checkout) will then execute scripts from the attacker-controlled path. The vulnerability is not merely malformed config output: GitPython's own writer converts embedded newlines into indented continuation lines, but Git still accepts an indented `[core]` stanza as a section header, so the injected `core.hooksPath` becomes effective configuration. This was found while auditing MLRun's `project.push()` method, which passes `author_name` and `author_email` directly to `config_writer().set_value()` with no sanitization. Both parameters cross a trust boundary — they are caller-supplied API inputs that end up in `.git/config`. PoC (standalone, no MLRun required): ```python import git, subprocess, os repo = git.Repo("/tmp/testrepo") with repo.config_writer() as cw: cw.set_value("user", "name", "foo\n[core]\nhooksPath=/tmp/hooks") r = subprocess.run(["git", "config", "core.hooksPath"], cwd="/tmp/testrepo", capture_output=True, text=True) assert r.returncode == 0 print(r.stdout.strip()) # /tmp/hooks os.makedirs("/tmp/hooks", exist_ok=True) open("/tmp/hooks/pre-commit", "w").write("#!/bin/sh\nid > /tmp/pwned\n") os.chmod("/tmp/hooks/pre-commit", 0o755) repo.index.add(["README"]) repo.git.commit(m="test") print(open("/tmp/pwned").read()) # uid=... ``` Tested on GitPython 3.1.46, git 2.39+. Impact: This is persistent repo config poisoning. Any user who can supply `author_name` or `author_email` to an application calling `config_writer().set_value()` can redirect Git hook execution to an arbitrary path. In a multi-user or hosted environment (e.g. a shared MLRun server where multiple users push to the same repositories), one user can poison the `.git/config` of a shared repo and have their hooks run in the context of every subsequent Git operation by any user. On single-user deployments, the impact depends on whether the application later invokes Git hooks automatically. Remediation: `set_value()` should raise on CR, LF, or NUL in values rather than silently pass them through: ```python import re if isinstance(value, (str, bytes)) and re.search(r"[\r\n\x00]", str(value)): raise ValueError("Git config values must not contain CR, LF, or NUL") ``` Rejecting is safer than stripping — a stripped newline might indicate the caller is passing unsanitized input at a higher level, and silent normalization masks that. Affected wherever `config_writer().set_value(section, key, user_input)` is called with external input.** GitPython is a dependency of DVC, MLflow, Kedro, and others — worth auditing their `set_value()` call sites for externally influenced inputs.

CVSS v3.1

Score 7.8high

Attack Vector
Local
Attack Complexity
Low
Privileges Required
Low
User Interaction
None
Scope
Unchanged
Confidentiality
High
Integrity
High
Availability
High
CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H

Affected software

Homebrewmore threats →ghsa
snakemake
pkg:brew/snakemake
Affected versions
>=5.5.3 <9.20.0

Run on your own infrastructure? Check whether these packages are installed with threat-finder — our free open-source scanner.

Technical Details

Gcve Source
db.gcve.eu
Osv Id
BREW-snakemake-CVE-2026-44244
Osv Schema Version
1.7.3
Ecosystems
["Homebrew"]
Cvss Version
3.1

Threat ID: 6aac8df755bf5e2cf54902f5

Added to database: 09/18/2026, 01:03:51 UTC

Last updated: 09/18/2026, 01:03:51 UTC

Views: 1

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