# Byte-compiled / optimized / DLL files
__pycache__/
*.py[codz]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py.cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# UV
#uv.lock

# Environments
.env
.envrc
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# Ruff stuff:
.ruff_cache/

# PyPI configuration file
.pypirc

# Cursor
.cursorignore
.cursorindexingignore

# =============================================================================
# Project-specific
# =============================================================================

# Data files (large, potentially sensitive)
data/*
!data/examples/
!data/review/
!data/fixtures/
!data/benchmarks/

# Local study/cohort data directories (keep local, not on remote)
data/examples/*/

# CDE data (large JSON, keep local)
data/examples/cde/

# Results and outputs
results/
outputs/
logs/

# Model artifacts
*.npy
*.faiss
*.bin
*.safetensors

# HuggingFace cache (models downloaded at runtime)
.cache/

# SQLite embedding cache
*.db
*.sqlite
*.sqlite3

# ddharmon runtime caches + pipeline run outputs (created by the notebooks)
.ddharmon/
harmonization_artifacts/

# Exported files
*.xlsx
*.csv
!data/examples/*.csv
!data/benchmarks/**/*.csv
!data/benchmarks/**/*.xlsx
!data/benchmarks/**/*.tsv

# Temp/lock files
*.tmp
.~lock.*

# Visualization outputs
*.png
*.pdf
!docs/**/*.pdf
!docs/**/*.png

# Local agent/session state — internal tooling, keep all of it local (not shipped)
.claude/

# Internal planning docs — local only, never shipped in the public package
docs/plans/
!data/examples/*.xlsx
