chore: Set up pre-commit hooks and fix linting issues

- Add pre-commit configuration with black, flake8, autoflake, mypy
- Fix trailing whitespace and end-of-file issues across all files
- Fix mypy error in tests/utils.py by handling return statements
- Format code with black for consistency
- All linting checks now pass

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

Co-Authored-By: Claude <[email protected]>

Author: nikolay-e

.github/workflows/cd.yml

@@ -217,4 +217,4 @@ jobs:
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
           echo "Attempting to merge tag ${{ needs.prepare-release.outputs.tag_name }} into main"
           git merge ${{ needs.prepare-release.outputs.tag_name }} --no-ff -m "Merge tag ${{ needs.prepare-release.outputs.tag_name }} into main"
-          git push origin main
+          git push origin main

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ on:
       - main
 
 jobs:
- 
+
   lint-type-check:
     name: Lint & Type Check
     runs-on: ubuntu-latest
@@ -28,7 +28,7 @@ jobs:
       - name: Cache pip Dependencies
         uses: actions/cache@v4
         with:
-         
+
           path: ~/.cache/pip
           key: ${{ runner.os }}-lint-pip-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
@@ -37,9 +37,9 @@ jobs:
       - name: Install Linters and Type Checker
         run: |
           python -m pip install --upgrade pip
-         
+
           pip install .[dev]
-         
+
 
       - name: Run Linters and Formatters Check
         run: |
@@ -48,10 +48,10 @@ jobs:
 
       - name: Run Type Checker (Mypy)
         run: |
-         
+
           mypy src tests
 
- 
+
   test:
     needs: lint-type-check
     strategy:
@@ -61,7 +61,7 @@ jobs:
         python-version: [ 3.9, '3.10', '3.11', '3.12' ]
 
     runs-on: ${{ matrix.os }}
-   
+
 
     steps:
       - name: Checkout Code
@@ -76,7 +76,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cache/pip
-         
+
           key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-${{ matrix.python-version }}-
@@ -85,36 +85,36 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-         
+
           pip install -e .[dev]
 
-     
+
 
       - name: Run Tests with Coverage
         run: |
-         
+
           pytest -v --cov=src/treemapper --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-       
+
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
         uses: codecov/codecov-action@v5
-       
-       
-       
+
+
+
         with:
            files: ./coverage.xml
            fail_ci_if_error: true
            verbose: true
 
- 
+
   test-pypy:
     needs: lint-type-check
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-       
+
         python-version: [ pypy-3.9, pypy-3.10 ]
 
     steps:
@@ -137,12 +137,12 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-         
+
           pip install -e .[dev]
-         
 
-     
+
+
 
       - name: Run Tests
         run: |
-          pytest -v
+          pytest -v

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+
+  - repo: https://github.com/psf/black
+    rev: 23.12.1
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: ['--config=.flake8']
+
+  - repo: https://github.com/pycqa/autoflake
+    rev: v2.2.1
+    hooks:
+      - id: autoflake
+        args: ['--remove-all-unused-imports', '--in-place']
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-PyYAML]
+        args: ['--ignore-missing-imports']

CHANGELOG.md

@@ -18,4 +18,4 @@
 ### Reliability Improvements
 - **Enhanced file permission handling**: Improved handling of permission-related errors for unreadable files and directories.
 - **Added WSL compatibility**: Added special handling for permission-related tests in Windows Subsystem for Linux (WSL) environments.
-- **Reduced verbosity**: Changed default verbosity level from INFO to ERROR to minimize console output unless errors occur.
+- **Reduced verbosity**: Changed default verbosity level from INFO to ERROR to minimize console output unless errors occur.

CLAUDE.md

@@ -111,4 +111,4 @@ python -m build
 
 # Create executable with PyInstaller
 pyinstaller treemapper.spec
-```
+```

README.md

@@ -4,8 +4,8 @@ A tool for converting directory structures to YAML format, designed for use with
 TreeMapper maps your entire codebase into a structured YAML file, making it easy to analyze code, document projects, and
 work with AI tools.
 
-[![Build Status](https://img.shields.io/github/actions/workflow/status/nikolay-e/TreeMapper/ci.yml)](https://github.com/nikolay-e/TreeMapper/actions)  
-[![PyPI](https://img.shields.io/pypi/v/treemapper)](https://pypi.org/project/treemapper)  
+[![Build Status](https://img.shields.io/github/actions/workflow/status/nikolay-e/TreeMapper/ci.yml)](https://github.com/nikolay-e/TreeMapper/actions)
+[![PyPI](https://img.shields.io/pypi/v/treemapper)](https://pypi.org/project/treemapper)
 [![License](https://img.shields.io/github/license/nikolay-e/TreeMapper)](https://github.com/nikolay-e/TreeMapper/blob/main/LICENSE)
 
 ## Installation
@@ -22,7 +22,7 @@ Generate a YAML tree of a directory:
 
 ```bash
 # Map current directory
-treemapper . 
+treemapper .
 
 # Map specific directory
 treemapper /path/to/dir
@@ -88,4 +88,4 @@ children:
 
 ## License
 
-Apache License 2.0 - see [LICENSE](LICENSE) for details.
+Apache License 2.0 - see [LICENSE](LICENSE) for details.

setup.cfg

@@ -1,4 +1,4 @@
 # setup.cfg
 
 [flake8]
-max-line-length = 130
+max-line-length = 130

src/treemapper/tree.py

@@ -154,7 +154,6 @@ def create_node(
             if children:
                 node["children"] = children
         elif node_type == "file":
-
             node_content: Optional[str] = None
             try:
                 # Try to read the file directly, and handle all possible errors

tests/conftest.py

@@ -92,17 +92,14 @@ def _set_perms(path: Path, perms: int):
 
     logging.debug(f"Cleaning up permissions for: {paths_changed}")
     for path in paths_changed:
-
         if path.exists() and path in original_perms:
             try:
-
                 if original_perms[path] is not None:
                     os.chmod(path, original_perms[path])
                     logging.debug(f"Restored permissions for {path}")
                 else:
                     logging.warning(f"Original permissions for {path} were None, not restoring.")
             except OSError as e:
-
                 logging.warning(f"Could not restore permissions for {path}: {e}")
 
 

tests/test_errors.py

@@ -89,7 +89,6 @@ def test_output_path_is_directory(temp_project, run_mapper, caplog):
     output_should_be_file.mkdir()
 
     with caplog.at_level(logging.ERROR):
-
         run_mapper([".", "-o", str(output_should_be_file)])
 
     assert any(