Destructive operation on submodules with submodule.recurse = true git setting #2063
Description
describe your issue
I added pre-commit to an ansible playbook repository that does extensive usage of git submodules for roles.
I had two submodules with extensive changes:
$ gst
On branch master
Your branch is ahead of 'origin/master' by 3 commits.
(use "git push" to publish your local commits)
...
modified: roles/dnscrypt-proxy (modified content) <-- submodule with extensive (non-commited) changes
modified: roles/syncthing (modified content) <-- another submodule with extensive (non-commited) changes
...Upon doing a commit I received an error (check ~/.cache/pre-commit/pre-commit.log section) due to having some problems in my repo and its submodules.
Notice that I cold not even run git status afterwards:
$ gst
fatal: not a git repository: roles/matomo/../../.git/modules/roles/matomoAfter fixing the problems:
$ rm -rf roles/matomo/ .git/modules/roles/matomo/
$ git submodule update
Cloning into '/home/apoc/w/posg-ops/roles/matomo'...
Submodule path 'roles/matomo': checked out '######'
fatal: could not get a repository handle for submodule 'roles/php'
$ rm -rf roles/php/ .git/modules/roles/php
$ git submodule update
Cloning into '/home/apoc/w/posg-ops/roles/php'...
Submodule path 'roles/php': checked out '######'and running git apply to have my changes back:
$ git apply /home/a666/.cache/pre-commit/patch1632709290-1076629I noticed that my two submodules now had no changes in them...
And unfortunately I see nothing in pre-commit cache area to help me recover them.
pre-commit --version
pre-commit 2.15.0
.pre-commit-config.yaml
---
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.0.1
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
- id: check-toml
- id: check-added-large-files
- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: 2.3.54
hooks:
- id: editorconfig-checker
- repo: https://github.com/antonbabenko/pre-commit-terraform
rev: v1.51.0
hooks:
- id: terraform_validate
- id: terraform_fmt
- id: checkov
- id: terrascan
- id: terraform_tfsec~/.cache/pre-commit/pre-commit.log (if present)
version information
pre-commit version: 2.15.0
sys.version:
3.9.7 (default, Aug 31 2021, 13:28:12)
[GCC 11.1.0]
sys.executable: /home/a666/.local/pipx/venvs/pre-commit/bin/python
os.name: posix
sys.platform: linux
error information
An unexpected error has occurred: CalledProcessError: command: ('/usr/lib/git-core/git', 'checkout', '--', '.')
return code: 255
expected return code: 0
stdout: (none)
stderr:
Migrating git directory of 'roles/fail2ban' from
'/home/a666/ops/roles/fail2ban/.git' to
'/home/a666/ops/.git/modules/roles/fail2ban'
fatal: not a git repository: ../../.git/modules/roles/matomo
error: Submodule 'roles/matomo' could not be updated.
Migrating git directory of 'roles/openproject' from
'/home/a666/ops/roles/openproject/.git' to
'/home/a666/ops/.git/modules/roles/openproject'
Migrating git directory of 'roles/oryhydra' from
'/home/a666/ops/roles/oryhydra/.git' to
'/home/a666/ops/.git/modules/roles/oryhydra'
fatal: not a git repository: ../../.git/modules/roles/php
error: Submodule 'roles/php' could not be updated.
Traceback (most recent call last):
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/error_handler.py", line 65, in error_handler
yield
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/main.py", line 368, in main
return hook_impl(
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/commands/hook_impl.py", line 237, in hook_impl
return retv | run(config, store, ns)
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/commands/run.py", line 399, in run
exit_stack.enter_context(staged_files_only(store.directory))
File "/usr/lib/python3.9/contextlib.py", line 448, in enter_context
result = _cm_type.__enter__(cm)
File "/usr/lib/python3.9/contextlib.py", line 119, in __enter__
return next(self.gen)
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/staged_files_only.py", line 92, in staged_files_only
with _intent_to_add_cleared(), _unstaged_changes_cleared(patch_dir):
File "/usr/lib/python3.9/contextlib.py", line 119, in __enter__
return next(self.gen)
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/staged_files_only.py", line 61, in _unstaged_changes_cleared
cmd_output_b('git', 'checkout', '--', '.', env=no_checkout_env)
File "/home/a666/.local/pipx/venvs/pre-commit/lib/python3.9/site-packages/pre_commit/util.py", line 154, in cmd_output_b
raise CalledProcessError(returncode, cmd, retcode, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('/usr/lib/git-core/git', 'checkout', '--', '.')
return code: 255
expected return code: 0
stdout: (none)
stderr:
Migrating git directory of 'roles/fail2ban' from
'/home/a666/ops/roles/fail2ban/.git' to
'/home/a666/ops/.git/modules/roles/fail2ban'
fatal: not a git repository: ../../.git/modules/roles/matomo
error: Submodule 'roles/matomo' could not be updated.
Migrating git directory of 'roles/openproject' from
'/home/a666/ops/roles/openproject/.git' to
'/home/a666/ops/.git/modules/roles/openproject'
Migrating git directory of 'roles/oryhydra' from
'/home/a666/ops/roles/oryhydra/.git' to
'/home/a666/ops/.git/modules/roles/oryhydra'
fatal: not a git repository: ../../.git/modules/roles/php
error: Submodule 'roles/php' could not be updated.