LICENSE
README.md
setup.py
autonima/__init__.py
autonima/__main__.py
autonima/cache_versions.py
autonima/cli.py
autonima/config.py
autonima/execution.py
autonima/meta.py
autonima/pipeline.py
autonima.egg-info/PKG-INFO
autonima.egg-info/SOURCES.txt
autonima.egg-info/dependency_links.txt
autonima.egg-info/entry_points.txt
autonima.egg-info/requires.txt
autonima.egg-info/top_level.txt
autonima/annotation/__init__.py
autonima/annotation/client.py
autonima/annotation/processor.py
autonima/annotation/prompts.py
autonima/annotation/schema.py
autonima/coordinates/__init__.py
autonima/coordinates/nimads_models.py
autonima/coordinates/openai_client.py
autonima/coordinates/parser.py
autonima/coordinates/processor.py
autonima/coordinates/prompts.py
autonima/coordinates/schema.py
autonima/llm/__init__.py
autonima/llm/client.py
autonima/llm/usage.py
autonima/models/__init__.py
autonima/models/types.py
autonima/retrieval/__init__.py
autonima/retrieval/base.py
autonima/retrieval/pubget.py
autonima/retrieval/utils.py
autonima/screening/__init__.py
autonima/screening/base.py
autonima/screening/openai_client.py
autonima/screening/prompts.py
autonima/screening/schema.py
autonima/screening/screener.py
autonima/search/__init__.py
autonima/search/base.py
autonima/search/pubmed.py
autonima/templates/__init__.py
autonima/templates/sample_config.yml
autonima/utils/__init__.py
autonima/utils/base.py
autonima/utils/criteria.py
autonima/webui/__init__.py
autonima/webui/app.py
autonima/webui/preferences.py
autonima/webui/progress.py
autonima/webui/runs.py
autonima/webui/secrets.py
autonima/webui/state.py
autonima/webui/static/app.jsx
autonima/webui/static/index.html
autonima/webui/static/styles.css
tests/test_ace_table_ingestion.py
tests/test_annotation_incremental_caching.py
tests/test_annotation_multi_analysis_validation.py
tests/test_annotation_retry.py
tests/test_basic.py
tests/test_cli.py
tests/test_confidence_reporting.py
tests/test_config_global_defaults.py
tests/test_coordinate_client.py
tests/test_coordinate_prompt.py
tests/test_criteria_mapping.py
tests/test_docs.py
tests/test_execution.py
tests/test_fulltext_incomplete_outputs.py
tests/test_fulltext_loading.py
tests/test_fulltext_screening.py
tests/test_llm_client.py
tests/test_llm_usage.py
tests/test_model_params.py
tests/test_multi_annotation.py
tests/test_nimads_annotations.py
tests/test_objective_in_prompt.py
tests/test_parallel_screening.py
tests/test_pipeline_retrieval.py
tests/test_pipeline_stage_cutoff.py
tests/test_pubmed.py
tests/test_retrieval.py
tests/test_screening.py
tests/test_simplified_screening.py
tests/test_webui.py
tests/test_webui_api.py