- Add .pre-commit-config.yaml with black, isort, flake8 hooks
- Configure black with 89 char line limit to match existing style
- Configure isort to be compatible with black
- Format entire codebase with black and isort
- Fix trailing whitespace and missing newlines
- Update CI workflows to use consistent linting
- Add pre-commit workflow for automated checks
- Add scripts for easy formatting and setup
- Update documentation with pre-commit instructions

All Python files now follow consistent formatting standards.

- Fix boolean comparisons (E712) - use 'is' instead of '=='
- Remove/comment unused imports (F401)
- Convert f-strings without placeholders to regular strings (F541)
- Replace bare except with specific exceptions (E722)
- Fix unused variables with comments or underscore (F841, B007)
- Fix lambda assignment to def (E731)
- Fix undefined names in __all__ (F822)
- Add docstrings for missing __init__ methods (D107)
- Fix block comment formatting (E265)
- Fix blank line formatting and whitespace (E306, W293, D202)
- Add per-file-ignores for complex functions (C901)
- Apply black formatting to ensure consistency

All 69 flake8 errors have been resolved, code is now fully compliant.

- Remove trailing whitespace from YAML and markdown files
- Fix line endings and formatting inconsistencies
- Apply black formatting to remaining Python files
- Clean up imports and whitespace

These changes were automatically applied by pre-commit hooks.

The pyproject.toml already contains coverage configuration in addopts,
so passing duplicate --cov arguments was causing conflicts.

- Add pytest-cov and pytest-xdist to dev dependencies
- Remove coverage configuration from pyproject.toml to avoid conflicts
- Keep coverage arguments only in GitHub Actions workflow

- Add windows module exports to locator/data/__init__.py
- Export generate_genomic_windows function for window analysis tests
- Fix numpy boolean comparison in test_model_persistence.py
- Convert numpy.True_ to Python bool before comparison

- Add tensorflow import for GPU detection
- Update GPU config test to handle case when GPU is not available
- In CI with CUDA_VISIBLE_DEVICES=-1, mixed precision is correctly disabled

- Change 'data/' to '/data/' and './data/' to only exclude top-level data directories
- Add windows.py to git tracking (was previously excluded)
- This fixes ModuleNotFoundError for locator.data.windows in CI

- WindowGenerator class does not exist in windows.py
- Only generate_genomic_windows function is available
- This fixes ImportError in all test files

- Make parallel module imports optional when Ray is not installed
- Add stub functions with helpful error messages for parallel methods
- Fix duplicate object description warning for PlottingMixin.plot_history
- This allows docs to build successfully without Ray dependency

- Prevent accidentally committing large output files from examples
- This directory contains generated plots and CSVs from demo runs

- Filter out harmless protobuf version warnings from TensorFlow
- Fix module path for parallel functions in api.rst (use locator.parallel not locator.parallel.parallel_analysis)
- The protobuf warnings are from TensorFlow/Google libraries and cannot be fixed by us
- Documentation should now build successfully