# Bytecode and artifacts
*.py[co]
*$py.class
*.so
__pycache__/
*.egg-info/
MANIFEST

# Standard build outputs
build/
dist/
develop-eggs/
downloads/
eggs/
.eggs/
sdist/
var/
wheels/
share/python-wheels/
lib/
lib64/
parts/
.installed.cfg
*.egg
*.manifest
*.spec
cython_debug/

# Dependency management
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
pip-log.txt
pip-delete-this-directory.txt
Pipfile.lock
uv.lock
poetry.lock
pdm.lock
.pdm.toml
.pdm-python
.pdm-build/
__pypackages__/
.python-version
pixi.lock
.pixi
node_modules/ # Node dependencies
package-lock.json

# Test and tooling caches
htmlcov/
.coverage
.coverage.*
nosetests.xml
coverage.xml
*.cover
*.py,cover
cover/
testing_folder/*
!testing_folder/inputs/
!testing_folder/inputs/**
!testing_folder/pytest.log
.cache/
.ruff_cache/
.tox/
.nox/
.hypothesis/
.pytest_cache/
.mypy_cache/
.dmypy.json
dmypy.json
.pyre/
.pytype/

# IDE and editor config
.idea/
.vscode/
.spyderproject
.spyproject
.ropeproject
.continueignore
.continuerules
.cursorignore
.cursorrules
.cursor
.continue
.pypirc

# Framework-specific files
local_settings.py
db.sqlite3
db.sqlite3-journal
instance/
.webassets-cache/
.scrapy/
celerybeat-schedule
celerybeat.pid
*.sage.py
.quarto/
public/
.ipynb_checkpoints/
profile_default/
ipython_config.py
docs/_build/
site/

# Logs and runtime outputs
data/
temp/
results/
logs/
*.log
log.txt
*logfile.log
*_logfile.txt
**/tmp/
**/tmp**

# PyBuilder outputs
.pybuilder/ 
target/

# Miscellaneous project files
# misc/
# notebooks/
reference.fasta
.crush
package.json
.gitignore
**taxdump**
.nfs*
rolypoly_data_slim_*.tar.gz
.github/copilot-instructions.md
benchmarking_outputs/*
benchmarking_logs/
dev_only/