feat: add pre-commit hooks for file formatting

Add pre-commit configuration with hooks to:
- Ensure all files end with single newline (end-of-file-fixer)
- Remove trailing whitespace (trailing-whitespace)
- Validate YAML and TOML syntax
- Prevent merge conflict markers

Integrate with existing hatch workflow and add CI job.
Include setup instructions in CLAUDE.md.

Applied automatic formatting fixes to existing files.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: dhellmann

.containerignore

@@ -12,4 +12,4 @@ build-logs/*
 sdists-repo/*
 venv*
 wheels-repo/*
-work-dir*/*
+work-dir*/*

.editorconfig

@@ -5,4 +5,4 @@ insert_final_newline = true
 trim_trailing_whitespace = true
 
 [*.md]
-trim_trailing_whitespace = false
+trim_trailing_whitespace = false

.github/workflows/check.yaml

@@ -5,6 +5,27 @@ on:
   - pull_request
 
 jobs:
+  pre-commit:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    if: ${{ !startsWith(github.ref, 'refs/tags') }}
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"  # minimum supported lang version
+
+      - name: Install dependencies
+        run: python -m pip install hatch 'click!=8.3.0'
+
+      - name: Run pre-commit hooks
+        run: hatch run lint:install-hooks && hatch run lint:check
+
   linter:
     name: linter
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer        # Ensures single trailing newline
+      - id: trailing-whitespace      # Removes trailing spaces
+        args: [--markdown-linebreak-ext=md]  # Preserve markdown line breaks
+      - id: check-yaml               # Validates YAML syntax
+      - id: check-merge-conflict     # Prevents merge conflict markers
+      - id: check-toml               # Validates TOML syntax

AGENTS.md

@@ -36,6 +36,13 @@
 
 ## Commands (IMPORTANT: Use File-Scoped First)
 
+### Setup Commands (Run Once)
+
+```bash
+# Install pre-commit hooks for automatic file formatting
+hatch run lint:install-hooks
+```
+
 ### File-Scoped Commands (PREFER THESE)
 
 ```bash
@@ -61,9 +68,19 @@ hatch run test:test <filepath> --log-level DEBUG
 hatch run lint:fix      # Format all code
 hatch run test:test     # Full test suite (slow!)
 hatch run mypy:check    # Type check everything
-hatch run lint:check    # Final lint check
+hatch run lint:check    # Final lint check (includes pre-commit hooks)
 ```
 
+### Pre-commit Hooks
+
+The project uses pre-commit hooks to automatically check file formatting:
+- **File endings**: Ensures all files end with a single newline
+- **Whitespace**: Removes trailing whitespace
+- **Syntax**: Validates YAML/TOML files
+- **Conflicts**: Prevents committing merge conflict markers
+
+These run automatically on commit if installed with `hatch run lint:install-hooks`.
+
 ## Safety and Permissions
 
 ### Allowed Without Asking

docs/concepts/index.rst

@@ -5,4 +5,3 @@ Concepts
    :maxdepth: 1
 
    dependencies
-

docs/example/overrides/patches/pydantic_core-2.18.4/0001-rust-version.patch

@@ -11,6 +11,6 @@
  ]
 -rust-version = "1.76"
 +rust-version = "1.75"
- 
+
  [dependencies]
  pyo3 = { version = "0.21.2", features = ["generate-import-lib", "num-bigint"] }

docs/how-tos/pyproject-overrides.rst

@@ -1,15 +1,15 @@
 Working with Complex pyproject.toml Requirements
 ================================================
 
-When using fromager's ``project_override`` feature (documented in the 
+When using fromager's ``project_override`` feature (documented in the
 :doc:`../customization` guide), there are some advanced scenarios worth
 understanding for complex build requirements.
 
 Handling Multiple Requirements for the Same Package
 ---------------------------------------------------
 
-When applying overrides, requirements are matched by (canonical) name, so updating 
-``numpy`` will affect all numpy requirements - all existing ones are replaced by 
+When applying overrides, requirements are matched by (canonical) name, so updating
+``numpy`` will affect all numpy requirements - all existing ones are replaced by
 the new requirements from the override, whether that's just one or multiple.
 
 Consider a ``pyproject.toml`` with multiple version-specific numpy requirements:
@@ -43,7 +43,7 @@ All existing numpy requirements are replaced by the single new one:
 
    [build-system]
    requires = [
-       "numpy==2.0.0", 
+       "numpy==2.0.0",
        "packaging",
        "setuptools==59.2.0; python_version<'3.12'",
        "setuptools<70.0.0; python_version>='3.12'"
@@ -58,7 +58,7 @@ When you apply overrides with multiple new numpy requirements:
 
    project_override:
      update_build_requires:
-       - setuptools 
+       - setuptools
        - numpy<3.0.0; python_version=='3.12'
        - numpy==3.0.0; python_version>'3.12'
 
@@ -72,4 +72,4 @@ All existing numpy requirements are replaced by all the new numpy requirements:
        "numpy==3.0.0; python_version>'3.12'",
        "packaging",
        "setuptools"
-   ]
+   ]

e2e/bootstrap_extras.txt

@@ -1,2 +1,2 @@
 requests[socks]==2.32.3
-stevedore ; python_version < "3.7"  # should not be included in output of test
+stevedore ; python_version < "3.7"  # should not be included in output of test

e2e/build-parallel/graph.json

@@ -308,4 +308,4 @@
       }
     ]
   }
-}
+}