.venv/
__pycache__/
*.pyc
*.egg-info/
dist/
build/
ivf/
# Java MetaMapLite output: contains UMLS-derived strings, do not commit
tests/parity/fixtures/
*.RRF
.pytest_cache/
.ruff_cache/
# examples/: the scripts, their README and their tests are source and ship. Everything they
# *produce* is UMLS-derived and does not -- annotation exports, the loaded databases and the
# filtered MRCONSO/MRREL extracts. Listed by extension rather than by name so a new export
# format is excluded by default: only .py, .md and the synthetic .txt notes are tracked.
examples/*.csv
examples/*.jsonl
examples/*.parquet
examples/*.db
examples/*.sqlite
examples/*.json

# annotation run output (examples/parse_to_*.py): verbatim note text and UMLS-derived
# strings, one directory per run. Never commit it.
out/
# corpora of notes to annotate: real ones are PHI, and even synthetic ones are not source
free_texts/

# local agent/tool state (a shared .claude/settings.json can still be committed)
# and per-user editor/notes vaults
.obsidian/
.claude/*.lock

# local credentials
.env
.env.*

# internal working document, not distributed
docs/DEVELOPMENT_PLAN.md

# internal working documents, not distributed
docs/OPERATIONS_MANUAL.md
docs/USER_GUIDE.md
docs/Negation detection.md
docs/Deploying to another machine.md
