# Python
__pycache__/
*.py[oc]
build/
dist/
wheels/
*.egg-info
.venv/

# Bundled native libraries (built during pip install)
python/zsasa/*.dylib
python/zsasa/*.so
python/zsasa/*.dll

# Zig
.zig-cache/
zig-out/

# Tool caches
.cache/
.ruff_cache/

# IDE
.idea/
.vscode/

# macOS
**/.DS_Store

# Temporary files
output.json
echo/
time/

# External benchmark dependencies (legacy locations)
freesasa-c/
rust-sasa-bench/

# Downloaded structure files for benchmark
benchmarks/cif/
benchmarks/alphafold_pdb/
data/*.cif
scripts/.venv/
scripts/uv.lock

# Benchmark results (raw data, too large to commit)
benchmarks/results/csv/
benchmarks/results/zig_*/
benchmarks/results/freesasa_*/
benchmarks/results/rust_*/
benchmarks/results/batch_*/
benchmarks/results/batch/*/temp_out/
benchmarks/results/python/

# Per-thread individual plots (generated, not doc-referenced)
benchmarks/results/plots/scatter/*/individual/
benchmarks/results/plots/speedup_by_bin/individual/
benchmarks/results/plots/efficiency/by_size.png

# Validation results (raw data; only .png plots are committed)
benchmarks/results/validation/**/config.json
benchmarks/results/validation/**/results.csv
benchmarks/results/validation_md/**/config.json
benchmarks/results/validation_md/**/results.csv

# Benchmark dataset (test JSON files)
benchmarks/dataset/

# Benchmark samples (large files)
benchmarks/samples/

# E. coli proteome dataset (AlphaFold structures)
benchmarks/UP000000625_83333_ECOLI_v6/

# SwissProt PDB dataset
benchmarks/swissprot_pdb_v6/
benchmarks/swissprot_pdb_v6.tar

# Human proteome dataset (AlphaFold structures)
benchmarks/UP000005640_9606_HUMAN_v6/
benchmarks/UP000005640_9606_HUMAN_v6.tar

# Archived benchmark results (v1: 100k PDB structures)
benchmarks/results_v1/

# E. coli benchmark temp files
benchmarks/ecoli_bench/temp_out/
benchmarks/ecoli_bench/results/
benchmarks/ecoli_bench/sasa_batch

# XTC reader cache files
test_data/.*.xtc_offsets.*

# Plans (local working files)
plans/

# Auto-generated Python API docs
docs/python-api/auto/

# MkDocs build output
site/

# Draft documents
docs/seminar-draft.md
docs/examples/
