__pycache__/
*.pyc
*.pyo
*.pyd
*.egg-info/
.dist-info/
.venv/
venv/
.env
.DS_Store
.ipynb_checkpoints/
build/
dist/
.coverage
.pytest_cache/
ruff_cache/

# artifacts
out/

# paper run logs (keep notebooks, ignore logs)
paper/source_data/out/logs/

# paper data (do not commit large/raw artifacts)
paper/source_data/**/raw/
paper/source_data/**/out/
paper/source_data/**/derived/**/.ipynb_checkpoints/

# (optional) ignore notebook checkpoints anywhere
**/.ipynb_checkpoints/

# -----------------------------
# gene ID mapping resources
# -----------------------------
# raw upstream files
resources/gene_id_maps/*.gtf
resources/gene_id_maps/*.gtf.gz
resources/gene_id_maps/*.gene_info
resources/gene_id_maps/*.gene_info.gz

# generated maps
resources/gene_id_maps/*id_map.tsv
# resources/gene_id_maps/*id_map.tsv.gz

# checksums (regen each time; not source)
resources/gene_id_maps/checksums.sha256

# Fig2 throwaway copies (including subfolders under fig/)
paper/source_data/**/fig/**/* copy*.pdf

# macOS / junk
.Trash-*
.DS_Store

/out/
/**/*.xlsx

paper/notebooks/**
!paper/notebooks/README.md

# keep journal Source Data workbooks
!paper/journal_source_data/SourceData_*.xlsx
!paper/journal_source_data/*.xlsx

# Excel temp files
~$*.xlsx

