# Runtime data + caches (large, gitignored per Step 1 of technical plan)
# Anchored to repo root — doesn't match dna_decode/data/ subpackage
# Ignore data/ contents per-entry (NOT the dir itself) so specific subdirs can be re-included
/data/*
# Exception: committed public reference alleles for the fungal-AMR real-data test (tiny GenBank CDS)
!/data/fungal_ref/
# Exception: committed Arabidopsis Path-B phenotype labels (small public AraPheno CSVs)
!/data/arabidopsis/
# Exception: committed public influenza N1 NA reference + real field alleles for the antiviral (4th-kingdom)
# real-data test (tiny GenBank CDS). Same class as fungal_ref.
!/data/antiviral_ref/
# Exception: committed public HIV-1 HXB2 RT CDS reference for the genome-mode caller self-check + planted-
# mutation test (tiny NCBI CDS, K03455.1:2550-4229). Same class as fungal_ref/antiviral_ref.
!/data/hiv_ref/
# Exception: committed public SARS-CoV-2 Mpro (nsp5) reference for the genome-mode caller integrity gate
# (tiny NCBI CDS, NC_045512.2:10055-10972). Same class as fungal_ref/antiviral_ref/hiv_ref.
!/data/sarscov2_ref/
*.h5
*.parquet
*.pkl
*.pt
*.bin

# Python
__pycache__/
*.pyc
*.pyo
*.egg-info/
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
.coverage.*
htmlcov/

# Environments
.venv/
venv/
env/
.env
.env.local

# IDE
.vscode/
.idea/
*.swp
.DS_Store

# Build outputs
build/
dist/
*.egg

# Model checkpoints (large, fetched from HuggingFace)
*.safetensors
*.ckpt
checkpoints/

# Logs
*.log
logs/

# Claude execute-plan scaffolding — recreated by /execute-plan runs
.claude/execute-plan-state/

# Generated audit / analysis reports (re-runnable via scripts/audit_cohort.py etc.)
/reports/

# AMRFinder runs (generated artifacts; tens of MB per strain)
/data/amrfinder_runs/

# Project-state scratch/working copies (stale duplicates of the live ledger; not history)
/project_state/*-scratch.md

# genome-map spike per-genome feature maps (large, regenerable via scripts/genome_map_spike.py)
wiki/genome_map_spike_*/
