.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

# Kept local, not published -- absent from GitHub and (hatchling honours this file) from the
# sdist: the corpus exporters, their comparator and run-directory helper, and the UMLS
# code-mapping scripts. Their tests live in tests/examples/local/ for the same reason, and run
# wherever the scripts exist.
examples/parse_to_csv.py
examples/parse_to_jsonl.py
examples/parse_to_jsonl_batch.py
examples/parse_to_parquet.py
examples/parse_to_sqlite.py
examples/compare_exports.py
examples/_runs.py
examples/add_icd10cm_codes.py
examples/add_icd10cm_hierarchy.py
examples/add_loinc_codes.py
examples/add_rxnorm_codes.py
examples/add_rxnorm_ingredients.py
examples/add_snomedct_hierarchy.py
examples/add_snomed_codes.py
examples/create_combined_codes_view.py
tests/examples/local/

# UMLS-derived working data: the filtered MRCONSO/MRREL extracts filter_mrconso.py and
# filter_mrrel.py write. Licensed material, and large -- it is yours to keep, not ours to
# redistribute.
data/

# annotation run output (the local examples/parse_to_*.py exporters): 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
