abhigyanpatwari/GitNexus · critical · ValueError

cannot inspect the clone for committed benchmark harness dat

Error message

cannot inspect the clone for committed benchmark harness data

What it means

Raised by sanitize_clone_for_hidden_oracles when `git ls-tree -d --format=%(objectname) HEAD -- eval/workflow_bench` fails (the run_managed result has ok=False). This probe checks whether the hidden benchmark harness tree is committed in HEAD; if git cannot even run the inspection, the sanitizer refuses to proceed because it cannot determine what needs to be removed.

Source

Thrown at eval/workflow_bench/oracle_assets.py:290

        raise ValueError("clone HEAD is not an immutable commit")

    hidden_tree_result = run_managed(
        [
            "git",
            "-C",
            str(root),
            "ls-tree",
            "-d",
            "--format=%(objectname)",
            "HEAD",
            "--",
            HIDDEN_HARNESS_PATH.as_posix(),
        ],
        timeout=60,
        tail_bytes=1024,
    )
    if not hidden_tree_result.ok:
        raise ValueError("cannot inspect the clone for committed benchmark harness data")
    hidden_tree = hidden_tree_result.stdout_tail.strip()
    if hidden_tree and (
        len(hidden_tree) not in {40, 64} or any(character not in "0123456789abcdefABCDEF" for character in hidden_tree)
    ):
        raise ValueError("committed benchmark harness is not a single bounded tree")

    current = root.joinpath(*HIDDEN_HARNESS_PATH.parts)
    if hidden_tree:
        parent = root
        for part in HIDDEN_HARNESS_PATH.parts:
            parent /= part
            try:
                metadata = parent.lstat()
            except OSError as exc:
                raise ValueError("committed benchmark harness is missing from the clone checkout") from exc
            if stat.S_ISLNK(metadata.st_mode) or not stat.S_ISDIR(metadata.st_mode):
                raise ValueError("benchmark harness checkout must contain only real directories")
    elif current.exists() or current.is_symlink():

View on GitHub (pinned to d540b00184)

Solutions

  1. Run `git -C <clone> fsck --full` and repair any reported corruption.
  2. Re-clone from source to obtain a clean object database.
  3. Check for git hooks (core.hooksPath) that might fail read-only commands and disable them for the clone.
  4. Ensure the object store is on a healthy, writable-enough filesystem.
Defensive patterns

Strategy: try-catch

Validate before calling

from eval.workflow_bench.oracle_assets import run_managed

def can_inspect_harness(clone) -> bool:
    res = run_managed(["git", "-C", str(clone), "ls-tree", "-d", "--format=%(objectname)", "HEAD", "--", "eval/workflow_bench"], timeout=60, tail_bytes=1024)
    return res.ok

Type guard

def clone_ls_tree_ok(clone) -> bool:
    from eval.workflow_bench.oracle_assets import run_managed
    res = run_managed(["git", "-C", str(clone), "ls-tree", "-d", "--format=%(objectname)", "HEAD", "--", "eval/workflow_bench"], timeout=60, tail_bytes=1024)
    return res.ok

Try / catch

try:
    head = sanitize_clone_for_hidden_oracles(clone)
except ValueError as exc:
    if "cannot inspect the clone" in str(exc):
        raise SystemExit("git ls-tree failed; run `git fsck --full` and re-clone") from exc
    raise

Prevention

When it happens

Trigger: The ls-tree invocation returns non-zero — e.g. the index/HEAD is in a bad state, a git subcommand crashed, the repository object database is corrupt, or a git hook/permission issue interferes with ls-tree.

Common situations: Repository corruption (run `git fsck --full`); a broken shallow clone; git hooks that reject read operations; filesystem errors on the object store; disk-full conditions during git operations.

Related errors

AI-assisted analysis of abhigyanpatwari/GitNexus@d540b00184 (2026-08-12). Data as JSON: /api/errors/e9e86904ba6e929f. Report an issue: GitHub.