Failed to run hook: No such file or directory (os error 2)

[hynek]

Hi,

this popular hook fails for me with this error:

$ uvx prek run --all-files -vvv ruff-check interrogate
DEBUG prek: 0.1.6 (2092da67d 2025-09-03)
DEBUG Git root: /Users/hynek/Work/vmws-manager
DEBUG Loading project configuration path=/Users/hynek/Work/vmws-manager/.pre-commit-config.yaml
TRACE Checking lock resource="store" path=/Users/hynek/.cache/prek/.lock
DEBUG Acquired lock resource="store"
DEBUG Hooks going to run: ["ruff-check", "interrogate"]
DEBUG Found installed environment for hook `ruff-check` at `/Users/hynek/.cache/prek/hooks/python-3s6AiFQXw77pGk55KtWq`
DEBUG Found installed environment for hook `interrogate` at `/Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D`
TRACE Released lock path=/Users/hynek/.cache/prek/.lock
TRACE Executing `/usr/bin/git ls-files -z`
DEBUG All files in the repo: 145
TRACE Files after filtered: 145
TRACE Executing `/usr/bin/git diff`
ruff check...............................................................TRACE Resolved command: /Users/hynek/.cache/prek/hooks/python-3s6AiFQXw77pGk55KtWq/bin/ruff
TRACE Running ruff-check total_files=123 concurrency=1
TRACE Executing `/Users/hynek/.cache/prek/hooks/python-3s6AiFQXw77pGk55KtWq/bin/ruff check --force-exclude --fix --exit-non-zero-on-fix --unsafe-fixes tests/adapters/test_sqlany.py src/vmws_manager/features/ui_auth/services.py [...]`
TRACE Executing `/usr/bin/git diff`
Passed
- hook id: ruff-check
- duration: 0.04s
  All checks passed!
interrogate..............................................................TRACE Resolved command: interrogate
TRACE Running interrogate total_files=123 concurrency=1
TRACE Executing `interrogate tests tests/adapters/test_sqlany.py src/vmws_manager/features/ui_auth/services.py tests/features/domains/__init__.py [...]`
error: Failed to run hook `interrogate`
  caused by: run command `python hook` failed
  caused by: No such file or directory (os error 2)

Looking at the executing, I see that it doesn't prepend the path like it does for Ruff (see also TRACE Resolved command: interrogate vs TRACE Resolved command: /Users/hynek/.cache/prek/hooks/python-3s6AiFQXw77pGk55KtWq/bin/ruff). The only difference in their definitions that I can spot it the language_version: python3.

[j178]

Hi, can you share the content of the .pre-commit-config.yaml file you have?

I tried it out but cann't reproduce the issue, here is what I got:

TRACE Resolved command: /Users/Jo/.cache/prek/hooks/python-31WuWdSi1hc4V87qU2k9/bin/interrogate
TRACE Found shebang: ["/Users/Jo/.cache/prek/hooks/python-31WuWdSi1hc4V87qU2k9/bin/python3"]
TRACE Resolved interpreter: /Users/Jo/.cache/prek/hooks/python-31WuWdSi1hc4V87qU2k9/bin/python3
TRACE Running interrogate total_files=1 concurrency=1
TRACE Executing `cd /private/tmp/test-ir && /Users/Jo/.cache/prek/hooks/python-31WuWdSi1hc4V87qU2k9/bin/python3 /Users/Jo/.cache/prek/hooks/python-31WuWdSi1hc4V87qU2k9/bin/interrogate t.py`

[hynek]

Huh that's odd! This is the whole file:

---

repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.12.12
    hooks:
      - id: ruff-check
        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
      - id: ruff-format

  - repo: https://github.com/astral-sh/uv-pre-commit
    rev: 0.8.15
    hooks:
      - id: uv-lock

  - repo: https://github.com/econchick/interrogate
    rev: 1.7.0
    hooks:
      - id: interrogate
        args: [tests]

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
        exclude: '.*\.(html|jinja|sql)'
      - id: check-toml
      - id: check-yaml

LMK if I can run some diagnostics for you.

[j178]

Can you take a look inside the directory /Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D? Maybe try running /Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D/bin/interrogate -h.

I suspect that the virtualenv might be corrupted.

[hynek]

Ah yes, looks like a blank virtualenv:

❯ eza /Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D
bin  CACHEDIR.TAG  lib  pyvenv.cfg

~
❯ eza /Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D/bin
activate  activate.bat  activate.csh  activate.fish  activate.nu  activate.ps1  activate_this.py  deactivate.bat  pydoc.bat  python  python3  python3.13

~
❯ eza /Users/hynek/.cache/prek/hooks/python-nNAk2DSDC9Iy4QQJpQ1D/lib/python3.13/site-packages/
__pycache__  _virtualenv.pth  _virtualenv.py

running prek clean seems to have fixed it. Not sure how it ended up like this, though, since I ran it in that directory and the other repos worked fine. oO

Would suggest to add some virtualenv health checks then, I guess. 🤓

Thanks!

[hynek]

JFTR, since it happened to me again, I have a suspicion that it might be related to me running it using uv run --with prek prek within a project.

I use that construction to make sure my hooks run with the correct Python version without configuring it explicitly. I switched to uvx for now, since I don't have the time to dig deeper. Edit I did dig a bit deeper, and this problem also happens if I install prek into the project virtualenv instead of globally (i.e., uv add --dev prek; uv run prek). uvx failed above because the virtualenv was already broken due to the uv run before it.

[j178]

reopening to see if anyone else is experiencing the same issue

[jamesbraza]

Seen during Future-House/paper-qa#1102's GitHub Actions run here inside of j178/prek-action@v1:

downloading prek 0.2.1 x86_64-unknown-linux-gnu
...
Cache hit for: prek-v1|Linux|X64|2713bf556179a7aeab8939a2a797f20ecb9af78f7766db4e4ecb48a98be4b678
...
Cache Size: ~80 MB (83880524 B)
...
Run prek run --show-diff-on-failure --color=always --all-files
...
error: Failed to run hook `check-case-conflict`
  caused by: run command `python hook` failed
  caused by: No such file or directory (os error 2)

I don't think this is a https://github.com/j178/prek-action issue, it's a prek issue.

Fwiw, I have the below .pre-commit-config.yaml:

default_language_version:
  python: python3
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - ...
      - id: check-case-conflict
      - ...

Perhaps this issue has to do with prek caching somehow?

[j178]

@jamesbraza For https://github.com/Future-House/paper-qa/actions/runs/17985538245/job/51162668574, I think it’s because setup-python was removed, so all the cached Python hooks virutalenv are now invalid (they’re still referencing a Python that was created by setup-python). I think we should prioritize #14 to avoid this issue.

[jamesbraza]

Today I moved another repo to prek, and was curious if this issue would recur there.

Without having setup-python there for the first prek-action run, these CI logs show:

• In a 3.11 parallel run: worked fine
• In a 3.13 parallel run: hit No such file or directory (os error 2)

Then adding back in setup-python, these CI logs show:

• In a 3.11 parallel run: hit No such file or directory (os error 2)
• In a 3.13 parallel run: hit No such file or directory (os error 2)

Both installed prek==0.2.2. So just sharing this statement, I don't think it's quite the full story yet:

I think it’s because setup-python was removed, so all the cached Python hooks virutalenv are now invalid (they’re still referencing a Python that was created by setup-python).