npm install git+file:// during hook install inside a submodule overwrites the submodule's index #3773
Description
search you tried in the issue tracker
GIT_INDEX_FILE, GIT_DIR, no_git_env, submodule, "unable to read", "invalid object", git+file, npm git
describe your issue
Since 4.6.1, when a language: node hook environment is installed by git commit run inside a git submodule, the submodule's index is replaced with the index of the hook repository. The commit fails and whatever was staged is lost. 4.6.0 is not affected: the reproduction below passes on 4.6.0 and on ff8541f, and fails on b1cc920 (#3719), 4.6.1 and 4.6.2.
Inside a submodule, git runs the pre-commit hook with absolute GIT_DIR and GIT_INDEX_FILE (<super>/.git/modules/<name> and <super>/.git/modules/<name>/index). #3719 changed the install to npm install ... git+file://<store clone>, and npm clones and checks out that URL with git. That git inherits GIT_INDEX_FILE, so the checkout writes the hook repository's index to the submodule's index file. store.py already runs the initial clone of the hook repository with no_git_env(). The npm install does not.
Confirm the issue on 4.6.2 using this Dockerfile:
FROM python:3.13
ARG PRE_COMMIT=pre-commit==4.6.2
RUN pip install "${PRE_COMMIT}"
RUN git config --global user.name repro \
&& git config --global user.email repro@example.com \
&& git config --global protocol.file.allow always
WORKDIR /repro
COPY <<'EOF' repro.sh
set -eu
pre-commit --version
git init -q sub
cd sub
cat > .pre-commit-config.yaml <<'YAML'
repos:
- repo: https://github.com/rbubley/mirrors-prettier
rev: v3.6.2
hooks:
- id: prettier
YAML
git add .pre-commit-config.yaml
git commit -q -m init
cd ..
git init -q super
cd super
git submodule -q add ../sub sub
git commit -q -m 'add submodule'
cd sub
pre-commit install
echo '# hello' > README.md
git add README.md
git commit -m 'trigger install from inside a submodule' || true
echo '--- submodule index (expected: .pre-commit-config.yaml, README.md)'
git ls-files -s
cat ~/.cache/pre-commit/pre-commit.log 2>/dev/null || true
EOF
CMD ["bash", "repro.sh"]docker build -t pre-commit-submodule-repro .
docker run --rm pre-commit-submodule-reprooutput of docker run (the pre-commit.log it prints at the end is in the log field below):
pre-commit 4.6.2
pre-commit installed at /repro/super/.git/modules/sub/hooks/pre-commit
[INFO] Initializing environment for https://github.com/rbubley/mirrors-prettier.
[INFO] Initializing environment for https://github.com/rbubley/mirrors-prettier:prettier@3.6.2.
[INFO] Installing environment for https://github.com/rbubley/mirrors-prettier.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('/usr/lib/git-core/git', 'diff', '--staged', '--name-only', '--no-ext-diff', '-z', '--diff-filter=ACMRTUXB')
return code: 128
stdout: (none)
stderr:
fatal: unable to read 7192ee1c223039c8ac42c8871ec7f6f8faeedebd
Check the log at /root/.cache/pre-commit/pre-commit.log
--- submodule index (expected: .pre-commit-config.yaml, README.md)
100644 7192ee1c223039c8ac42c8871ec7f6f8faeedebd 0 .github/workflows/main.yml
100644 72e8ffc0db8aad71a934dd11e5968bd5109e54b4 0 .npmignore
100644 a7d109de0c111bd5b225d20183593b283ad80516 0 .pre-commit-hooks.yaml
100644 b72762837ea636398fece3c5651f664c2ee82ffb 0 .version
100644 d86d9ea06347dbd79c04079484155ea94fa2c3ed 0 LICENSE
100644 92a483e6ca5ae20de5bae985aa1215eb658c6498 0 README.md
100644 d4083c5b452e10dc41112eae1813d9d1631024b5 0 package.json
The submodule's index now holds the files of mirrors-prettier. git read-tree HEAD in the submodule recovers it.
Confirm 4.6.0 is not affected:
docker build --build-arg PRE_COMMIT=pre-commit==4.6.0 -t pre-commit-submodule-repro:4.6.0 .
docker run --rm pre-commit-submodule-repro:4.6.0Workaround: run pre-commit install-hooks from a shell before committing.
The closest related issues I found is #1379 which has the same fatal: unable to read <sha> after a fresh install; the cause was never found for this one.
pre-commit --version
pre-commit 4.6.2
.pre-commit-config.yaml
repos:
- repo: https://github.com/rbubley/mirrors-prettier
rev: v3.6.2
hooks:
- id: prettier~/.cache/pre-commit/pre-commit.log (if present)
version information
pre-commit version: 4.6.2
git --version: git version 2.47.3
sys.version:
3.13.16 (main, Oct 6 2026, 04:43:07) [GCC 14.2.0]
sys.executable: /usr/local/bin/python3.13
os.name: posix
sys.platform: linux
error information
An unexpected error has occurred: CalledProcessError: command: ('/usr/lib/git-core/git', 'diff', '--staged', '--name-only', '--no-ext-diff', '-z', '--diff-filter=ACMRTUXB')
return code: 128
stdout: (none)
stderr:
fatal: unable to read 7192ee1c223039c8ac42c8871ec7f6f8faeedebd
Traceback (most recent call last):
File "/usr/local/lib/python3.13/site-packages/pre_commit/error_handler.py", line 73, in error_handler
yield
File "/usr/local/lib/python3.13/site-packages/pre_commit/main.py", line 401, in main
return hook_impl(
store,
...<5 lines>...
args=args.rest[1:],
)
File "/usr/local/lib/python3.13/site-packages/pre_commit/commands/hook_impl.py", line 275, in hook_impl
return retv | run(config, store, ns)
~~~^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.13/site-packages/pre_commit/commands/run.py", line 445, in run
return _run_hooks(config, hooks, skips, args)
File "/usr/local/lib/python3.13/site-packages/pre_commit/commands/run.py", line 291, in _run_hooks
_all_filenames(args), config['files'], config['exclude'],
~~~~~~~~~~~~~~^^^^^^
File "/usr/local/lib/python3.13/site-packages/pre_commit/commands/run.py", line 271, in _all_filenames
return git.get_staged_files()
~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.13/site-packages/pre_commit/git.py", line 137, in get_staged_files
cmd_output(
~~~~~~~~~~^
'git', 'diff', '--staged', '--name-only', '--no-ext-diff', '-z',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...<2 lines>...
cwd=cwd,
^^^^^^^^
)[1],
^
File "/usr/local/lib/python3.13/site-packages/pre_commit/util.py", line 117, in cmd_output
returncode, stdout_b, stderr_b = cmd_output_b(*cmd, **kwargs)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.13/site-packages/pre_commit/util.py", line 111, in cmd_output_b
raise CalledProcessError(returncode, cmd, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('/usr/lib/git-core/git', 'diff', '--staged', '--name-only', '--no-ext-diff', '-z', '--diff-filter=ACMRTUXB')
return code: 128
stdout: (none)
stderr:
fatal: unable to read 7192ee1c223039c8ac42c8871ec7f6f8faeedebd
Activity
Tycorc commented on Oct 11, 2026
This isn't limited to submodules: it happens whenever git hands the hook an absolute GIT_INDEX_FILE, which it also does for git commit -a (the temporary index.lock) and for any commit in a linked worktree (.git/worktrees/<name>/index). It needs a node hook whose environment isn't installed yet, so it shows up on a fresh cache or after a rev bump.
Plain repo, no Docker (pre-commit 4.6.2, git 2.54, node 22):
The commit aborts once the lock file holds the hook repository's index. The same steps in a git worktree add checkout commit nothing and leave git ls-files listing package.json, .pre-commit-hooks.yaml and the rest of mirrors-prettier until git read-tree HEAD.
#3774 as it stands fixes both cases for me.
chore: Update pre-commit hooks
chore: Update pre-commit hooks
chore: Update pre-commit hooks
chore: Update pre-commit hooks