# virtual environments
.venv/
.venv_linux/
venv/
venv_linux/

# IDE
.vscode/

# Python
__pycache__/
*.pyc
.pytest_cache/
numba_cache/

# packaging artifacts
build/
dist/
*.egg-info/
.eggs/
*.whl

# datasets — download separately via Zenodo (see README)
data/
zenodo/data/

# zenodo/ subdirs downloaded or generated (not committed)
zenodo/raw_simulation_results/
zenodo/raw_simulation_results_dt/
zenodo/simulation_scores/
zenodo/simulation_scores_dt/
zenodo/tree_metrics/
zenodo/*.zip

# generated outputs — reproduced by running the scripts
real-data-bias-analysis/
bias-analysis/
paper_outputs/
cache_nd/

# stale / superseded files
all_sims.csv
all_sims_trimmed.csv
ndscape_repo.7z
# optional JSON conversion of simulation_configs.csv
simulation_configs.json
zenodo/simulation_configs.json

# temp file written by reproduce.py --steps sim/moran --classes ...
_selected_sims.csv

# credentials — never commit these
.env
.pypirc
*.pypirc
