.gitignore

# Reference directory
reference/

# Rust build artifacts
target/
Cargo.lock
**/*.rs.bk
debug/
release/
*.rlib

# Python build artifacts
python/__pycache__/
python/*.pyc
python/*.pyo
python/*.pyd
python/.pytest_cache/
python/.coverage
python/htmlcov/
python/build/
python/dist/
python/*.egg-info/
python/.venv
python/venv
python/.mypy_cache
python/.tox

# IDE files
.idea/
.vscode/
*.swp
*.swo
*~

# OS files
.DS_Store
Thumbs.db

# Environment variables
.env
.env.local
.env.*.local

# Logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
*.prof*
*.d
*.pdb

# Output files
*.jf
*.rk
*.txt
*.rkdb

# Except test data files that should be tracked
!python/tests/test_data/*.rkdb
!python/tests/test_data/*.rk
# Golden regression fixtures (plan 01-03, decision D-11) — committed binary
# baselines; sha256 sidecars in tests/fixtures/golden_manifest.sha256 detect
# any tampering or byte drift at test time.
!tests/fixtures/golden_*.rkdb
!tests/fixtures/legacy_v2_offset42.rkdb

# Examples output and data
examples/output/
examples/data/*.fa
examples/data/*.fa.gz
!examples/data/small_dataset.fa

# Test and temporary files (stored in /Users/forrest/Temp/demodata/)
test_output/
temp_files/

# IDE files
.vscode/
.idea/
*.swp
*.swo

# OS files
.DS_Store
Thumbs.db

# Logs
*.log

# Environment files
.env*
!.env.example

# Benchmark results
benches/
criterion/

# Test coverage
tarpaulin-report.html
coverage/
coverage.xml
*.xml

# Added by cargo

/target

# Rust build artifacts
/target/
**/*.rs.bk
Cargo.lock

# Python cache and temp files
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Python compiled modules (including rustkmer)
python/rustkmer/*.so
python/rustkmer/*.cpython-*.so
#
.claude/
.serena/
.spekrit/
.specify/

# Documentation build
site/
docs/venv/
docs/_build/

# Temporary scripts
check_rustkmer_methods.py
fix_warnings.py
IMPLEMENTATION_STATUS.md

# Large test data
tests/python/fixtures/large_scale/sequence_xlarge.fa
tests/python/fixtures/large_scale/rnaseq_reads.fq.gz

# Benchmarks directory (removed due to non-compliant code)
benches/

# IDE files
.vscode/
.idea/
*.swp
*.swo
*~

# OS generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# Performance profiling files
*.prof
*.profraw

# Backup files
*.bak
*.backup
*.old
*.orig
*.tmp
*.temp

# Documentation build
site/
docs/.doctrees/
*.doctree

# MkDocs build output
mkdocs.yml.local

# Python wheel builds
*.whl
wheelhouse/

.venv/
examples/marimo/__marimo__/

tmp/



# Tool-specific cache files (can be large)
.serena/
.venv/

.venv*/

# Hypothesis testing cache (property-based testing)
.hypothesis/
.pytest_cache/
# Test databases
*.rkd
*.rkb

# Test binaries
test_memory
test_memory_fixed

# Temporary merge files
ext_sort_*
external_sort_*

# Debug files
*.tmp
merged_test*.rkd