LICENSE
README.md
pyproject.toml
src/trialmatchai/__init__.py
src/trialmatchai/__main__.py
src/trialmatchai/main.py
src/trialmatchai/orchestration.py
src/trialmatchai/pipeline.py
src/trialmatchai.egg-info/PKG-INFO
src/trialmatchai.egg-info/SOURCES.txt
src/trialmatchai.egg-info/dependency_links.txt
src/trialmatchai.egg-info/entry_points.txt
src/trialmatchai.egg-info/requires.txt
src/trialmatchai.egg-info/top_level.txt
src/trialmatchai/cli/__init__.py
src/trialmatchai/cli/bootstrap_data.py
src/trialmatchai/cli/build.py
src/trialmatchai/cli/build_concepts.py
src/trialmatchai/cli/e2e.py
src/trialmatchai/cli/healthcheck.py
src/trialmatchai/cli/import_patient.py
src/trialmatchai/cli/index_data.py
src/trialmatchai/cli/main.py
src/trialmatchai/cli/pipeline.py
src/trialmatchai/cli/run.py
src/trialmatchai/cli/trec.py
src/trialmatchai/cli/update_registry.py
src/trialmatchai/config/__init__.py
src/trialmatchai/config/config.json
src/trialmatchai/config/config_loader.py
src/trialmatchai/config/settings.py
src/trialmatchai/constraints/__init__.py
src/trialmatchai/constraints/evaluation.py
src/trialmatchai/constraints/extraction.py
src/trialmatchai/constraints/models.py
src/trialmatchai/constraints/reports.py
src/trialmatchai/entities/__init__.py
src/trialmatchai/entities/annotator.py
src/trialmatchai/entities/builder.py
src/trialmatchai/entities/concept_sources.py
src/trialmatchai/entities/linker.py
src/trialmatchai/entities/recognizers.py
src/trialmatchai/entities/schemas.py
src/trialmatchai/entities/types.py
src/trialmatchai/entities/resources/variant_patterns.tsv
src/trialmatchai/entity_schemas/trialmatchai.yaml
src/trialmatchai/finetuning/__init__.py
src/trialmatchai/finetuning/_sft.py
src/trialmatchai/finetuning/cli.py
src/trialmatchai/finetuning/config.py
src/trialmatchai/finetuning/cot.py
src/trialmatchai/finetuning/data.py
src/trialmatchai/finetuning/merge.py
src/trialmatchai/finetuning/ner.py
src/trialmatchai/finetuning/reranker.py
src/trialmatchai/interop/__init__.py
src/trialmatchai/interop/detect.py
src/trialmatchai/interop/models.py
src/trialmatchai/interop/narrative.py
src/trialmatchai/interop/utils.py
src/trialmatchai/interop/exporters/__init__.py
src/trialmatchai/interop/exporters/fhir.py
src/trialmatchai/interop/exporters/matching_summary.py
src/trialmatchai/interop/exporters/phenopacket.py
src/trialmatchai/interop/importers/__init__.py
src/trialmatchai/interop/importers/fhir.py
src/trialmatchai/interop/importers/omop.py
src/trialmatchai/interop/importers/phenopacket.py
src/trialmatchai/interop/importers/text.py
src/trialmatchai/matching/__init__.py
src/trialmatchai/matching/eligibility_base.py
src/trialmatchai/matching/eligibility_reasoning_transformers.py
src/trialmatchai/matching/eligibility_reasoning_vllm.py
src/trialmatchai/matching/query_expansion.py
src/trialmatchai/matching/trial_ranker.py
src/trialmatchai/matching/retrieval/__init__.py
src/trialmatchai/matching/retrieval/criteria_retrieval.py
src/trialmatchai/matching/retrieval/first_level_planner.py
src/trialmatchai/matching/retrieval/location.py
src/trialmatchai/matching/retrieval/synonyms.py
src/trialmatchai/matching/retrieval/trial_retrieval.py
src/trialmatchai/models/__init__.py
src/trialmatchai/models/embedding/__init__.py
src/trialmatchai/models/embedding/text_embedder.py
src/trialmatchai/models/llm/__init__.py
src/trialmatchai/models/llm/llm_reranker.py
src/trialmatchai/models/llm/transformers_reranker.py
src/trialmatchai/models/llm/vllm_loader.py
src/trialmatchai/registry/__init__.py
src/trialmatchai/registry/clinicaltrials_gov.py
src/trialmatchai/registry/criteria_chunking.py
src/trialmatchai/registry/defaults.py
src/trialmatchai/registry/manifest.py
src/trialmatchai/registry/normalization.py
src/trialmatchai/registry/preparation.py
src/trialmatchai/registry/updater.py
src/trialmatchai/schemas/__init__.py
src/trialmatchai/schemas/phenopacket.py
src/trialmatchai/search/__init__.py
src/trialmatchai/search/lancedb_backend.py
src/trialmatchai/services/__init__.py
src/trialmatchai/services/preflight.py
src/trialmatchai/trec/__init__.py
src/trialmatchai/trec/corpus.py
src/trialmatchai/trec/metrics.py
src/trialmatchai/trec/qrels.py
src/trialmatchai/trec/runner.py
src/trialmatchai/trec/topics.py
src/trialmatchai/utils/__init__.py
src/trialmatchai/utils/file_utils.py
src/trialmatchai/utils/json_utils.py
src/trialmatchai/utils/logging_config.py
src/trialmatchai/utils/temporal_utils.py
src/trialmatchai/utils/text.py
src/trialmatchai/utils/timing.py
tests/test_bootstrap_data.py
tests/test_concept_sources.py
tests/test_config_pytest.py
tests/test_constraints.py
tests/test_criteria_chunking.py
tests/test_deployment_readiness.py
tests/test_embedding.py
tests/test_entities.py
tests/test_fhir_robustness.py
tests/test_file_utils_pytest.py
tests/test_finetuning.py
tests/test_first_level_planner.py
tests/test_first_level_search_pytest.py
tests/test_import_patient_cli.py
tests/test_lancedb_search_backend.py
tests/test_location_filter.py
tests/test_logging.py
tests/test_logging_pytest.py
tests/test_metrics.py
tests/test_package_imports.py
tests/test_patient_interop.py
tests/test_patient_runtime_loading.py
tests/test_pipeline.py
tests/test_preflight_and_indexer.py
tests/test_qrels_eval.py
tests/test_registry_updater.py
tests/test_schemas.py
tests/test_search_queries_pytest.py
tests/test_second_level_search_pytest.py
tests/test_settings.py
tests/test_trec_reproduction.py
tests/test_trial_ranker_pytest.py
tests/test_trial_ranker_scoring_contract.py
tests/test_trial_ranker_tiebreak.py
tests/test_variant_recognizer.py