# macOS / editor state
.DS_Store
.AppleDouble
.LSOverride
._*
.idea/
.vscode/
*.swp
*.swo

# Python environments and local config
.venv/
.env
.env.*
!.env.example
.python-version.local

# Local agent/tool runtime payloads
.agent/
.claude/
.codex/
.opencode/

# Python caches and tooling
__pycache__/
*.py[cod]
*$py.class
.pytest_cache/
.ruff_cache/
.mypy_cache/
.pyre/
.tox/
.coverage
.coverage.*
coverage.xml
htmlcov/

# Build and packaging outputs
build/
dist/
*.egg-info/
*.egg
wheelhouse/

# Jupyter
.ipynb_checkpoints/
*/.ipynb_checkpoints/

# Local generated science/benchmark outputs. generated MLX and OpenMM reference outputs are ignored.
# Keep only small fixtures that a future spec approves.
artifacts/
outputs/
results/
scratch/
tmp/
*.npy
*.npz
*.h5
*.hdf5
*.xyz
*.traj
notebooks/ligand-receptor-motion/data/cache/
notebooks/ligand-receptor-motion/data/gpcrmd-cache/
notebooks/ligand-receptor-motion/data/gpcrmd-mlx/
notebooks/ligand-receptor-motion/data/mlx-real-md/
notebooks/ligand-receptor-motion/data/openmm-md/
notebooks/ligand-receptor-motion/data/openmm-preview/
notebooks/ligand-receptor-motion/data/prepared/
notebooks/ligand-receptor-motion/data/processed/
notebooks/archive/atp-pocket-mlx-demo/data/prepared/

# Reference checkouts only — fetched locally, never tracked.
vendors/

# Auto-generated API reference pages (Griffe → Starlight). Build artifact:
# regenerated from src/ by scripts/gen_api_docs.py on every build.
site/src/content/docs/api/

# Astro / Starlight build state
site/.astro/
site/node_modules/
