# Virtual environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# FGCZ and Local Development files
scripts/
benchmarks/**/*.R
benchmarks/**/*.sh
test_*.py
!tests/test_*.py
*debug*.py
*.qmd
*.html
!docs/tutorial.html
!docs/index.html

# Lockfiles
uv.lock
# Python
__pycache__/
*.pyc
*.pyo
*.egg-info/
dist/
build/

# Testing
.pytest_cache/
htmlcov/
.coverage
coverage.xml

# Data (large reference/validation files)
data/

# Keep test fixtures (small R reference outputs for concordance tests)
!tests/fixtures/

# R reference validation data
scripts/r_reference/

# Package data (keep q_matrices.npz, ignore everything else)
src/rctd/data/*
!src/rctd/data/q_matrices.npz

# IDE
.vscode/
.idea/

# OS
.DS_Store
Thumbs.db

# SLURM / HPC
*.log
*.err
/scratch/

# Development / benchmark scripts (FGCZ-internal, not for public distribution)
scripts/
test_py.py
vignette_bench.sh
analysis_region3.html
analysis_region1.qmd
analysis_region1.html
check.py

# Credentials / local secrets
.env
.env.local
.env.*.local
*.key
*.pem
secrets/
.netrc

# Build artifacts
*.knit.md

# Generated version file
src/rctd/_version.py
docs/plans/
!docs/plans/100-percent-matching-roadmap.md
