pre-commit in CI fails with 'files were modified by this hook' (e.g. trailing-whitespace, end-of-file-fixer, black). How do I fix it?

Cause: Many pre-commit hooks auto-fix files. A hook fails when it modifies files, so the commit or CI run stops and you are expected to review and re-add the changes. In CI the changes are made in the throwaway checkout, so the job just goes red, meaning the pushed commit was not already formatted. Fix: 1. Run it locally on the same files: "pre-commit run --all-files" (or "pre-commit run --from-ref origin/main --to-ref HEAD" for changed files), then git add the modified files and commit. Install the git hook with "pre-commit install" so it runs before every commit in future. 2. In CI, run "pre-commit run --all-files --show-diff-on-failure" so the log prints exactly what the hooks would change. 3. Make versions agree: pin hook revisions in .pre-commit-config.yaml and run "pre-commit autoupdate" deliberately; a local tool version differing from the hook's pinned one can produce endless diffs. 4. Cache ~/.cache/pre-commit between CI runs to avoid reinstalling hook environments. 5. Optionally use pre-commit.ci, which runs hooks without extra setup and can autofix pull requests and periodically update hook versions. 6. Do not skip the failing hook with SKIP or --no-verify in CI as the fix; that only hides the formatting drift. Verify: running "pre-commit run --all-files" a second time locally reports Passed for every hook with no files changed, and the CI job is green. Sources: https://pre-commit.com/ https://github.com/pre-commit/action