# --- Python ---
__pycache__/
*.py[cod]
*.egg-info/
*.egg
.eggs/
dist/
build/
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
coverage.xml
htmlcov/
.venv/
venv/
.ipynb_checkpoints/

# --- Third-party datasets: never committed, cited instead ---
# These come from 10x Genomics, CELLxGENE, figshare/scIB, Zenodo (Zhao et al.
# 2025), CraftedExperiment (Liu et al. 2025) and CellBRF. We have no right to
# redistribute them, several files exceed GitHub's 100 MB per-file limit, and the
# tree is ~5.6 GB. Sources and accessions: docs/DATA_SOURCES.md
data/
examples/data/

# Belt and braces: raw matrix / archive formats anywhere in the tree.
*.h5ad
*.h5
*.rds
*.RData
*.mtx
*.mtx.gz
*.loom
*.zip
*.tar
*.tar.gz
*.tgz
*.txt.gz
*.csv.gz
*.xlsx

# --- Locally generated outputs: not committed ---
# Every table, figure and log under here is produced by the benchmark scripts.
examples/results/

# --- Local research notes (not part of the public docs site / release) ---
# Keep on disk for development; do not publish to GitHub / RTD / PyPI sdist.
docs/PAPER_*
docs/DEVELOPMENT_LOG.md
docs/PACKAGE_VALUE.md
docs/gold.md
docs/review.md
docs/AUTO_N_*
docs/CELLBRF_*
docs/DATA_SOURCES.md
docs/**/*.csv

# Sphinx build products
docs/_build/
docs/api/generated/

# --- Editors / OS ---
.DS_Store
*.swp
*~
.idea/
.vscode/

# Claude Code harness internals
.claude/
