.gitignore
.pre-commit-config.yaml
CONTRIBUTING.md
LICENSE
README.md
conftest.py
env.example.sh
pyproject.toml
uv.lock
.github/actions/setup/action.yaml
.github/workflows/code-quality-main.yaml
.github/workflows/code-quality-pr.yaml
.github/workflows/python-build.yaml
.github/workflows/tests.yaml
docs/MULTITASK.md
docs/REPO_CLEANUP_PLAN.md
scripts/bench_multitask_dataset.py
src/EveryQuery.egg-info/PKG-INFO
src/EveryQuery.egg-info/SOURCES.txt
src/EveryQuery.egg-info/dependency_links.txt
src/EveryQuery.egg-info/entry_points.txt
src/EveryQuery.egg-info/requires.txt
src/EveryQuery.egg-info/scm_file_list.json
src/EveryQuery.egg-info/scm_version.json
src/EveryQuery.egg-info/top_level.txt
src/every_query/README.md
src/every_query/__init__.py
src/every_query/data/README.md
src/every_query/data/__init__.py
src/every_query/data/build_ontology.py
src/every_query/data/conditional_multitask_datamodule.py
src/every_query/data/datamodule.py
src/every_query/data/dataset.py
src/every_query/data/multitask_dataset.py
src/every_query/data/multitask_eval_dataset.py
src/every_query/data/ontology.py
src/every_query/data/query_seq_dataset.py
src/every_query/data/query_seq_task.py
src/every_query/data/rope_time.py
src/every_query/data/schema.py
src/every_query/data/configs/build_ontology.yaml
src/every_query/evaluate/README.md
src/every_query/evaluate/__init__.py
src/every_query/evaluate/evaluate.py
src/every_query/evaluate/evaluate_multitask.py
src/every_query/evaluate/metrics.py
src/every_query/evaluate/configs/evaluate.yaml
src/every_query/evaluate/configs/evaluate_multitask.yaml
src/every_query/generate_tasks/README.md
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src/every_query/generate_tasks/interval_table.py
src/every_query/generate_tasks/query_sequence_labeling.py
src/every_query/generate_tasks/redesign-spec.md
src/every_query/generate_tasks/sample_evaluation_query_sequences.py
src/every_query/generate_tasks/sample_evaluation_tasks.py
src/every_query/generate_tasks/sample_multitask_sequences.py
src/every_query/generate_tasks/sample_task_tracking_pairs.py
src/every_query/generate_tasks/sample_tasks.py
src/every_query/generate_tasks/configs/sample_evaluation_query_sequences_config.yaml
src/every_query/generate_tasks/configs/sample_evaluation_tasks_config.yaml
src/every_query/generate_tasks/configs/sample_multitask_sequences_config.yaml
src/every_query/generate_tasks/configs/sample_query_sequences_config.yaml
src/every_query/generate_tasks/configs/sample_task_tracking_pairs_config.yaml
src/every_query/generate_tasks/configs/sample_training_tasks_config.yaml
src/every_query/model/README.md
src/every_query/model/__init__.py
src/every_query/model/answers.py
src/every_query/model/conditional_multitask_ar_model.py
src/every_query/model/conditional_multitask_lightning.py
src/every_query/model/lightning_module.py
src/every_query/model/model.py
src/every_query/model/ontology_embedding.py
src/every_query/model/task_auroc_callback.py
src/every_query/predict/README.md
src/every_query/predict/__init__.py
src/every_query/predict/predict.py
src/every_query/predict/predict_multitask.py
src/every_query/predict/schema.py
src/every_query/predict/configs/predict.yaml
src/every_query/predict/configs/predict_multitask.yaml
src/every_query/predict/external_tasks/README.md
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src/every_query/predict/external_tasks/aces_to_eq.py
src/every_query/predict/external_tasks/get_per_code_from_composite.py
src/every_query/predict/external_tasks/process_composite.py
src/every_query/predict/external_tasks/configs/aces_to_eq.yaml
src/every_query/predict/external_tasks/configs/get_per_code_from_composite_config.yaml
src/every_query/predict/external_tasks/configs/process_composite_config.yaml
src/every_query/preprocessing/__init__.py
src/every_query/preprocessing/__main__.py
src/every_query/preprocessing/configs/_data.yaml
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src/every_query/preprocessing/configs/_reshard_data.yaml
src/every_query/train/README.md
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src/every_query/train/resume_check.py
src/every_query/train/train.py
src/every_query/train/configs/_demo_train.yaml
src/every_query/train/configs/_demo_train_conditional_multitask_ar.yaml
src/every_query/train/configs/conditional_multitask_ar_config.yaml
src/every_query/train/configs/config.yaml
src/every_query/train/configs/fast_config.yaml
src/every_query/train/configs/callbacks/task_auroc.yaml
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src/every_query/utils/codes.py
src/every_query/utils/digest.py
src/every_query/utils/model_loader.py
src/every_query/utils/seeds.py
tests/README.md
tests/__init__.py
tests/designed_specs.py
tests/test_cli_smoke.py
tests/test_conditional_multitask_ar_model.py
tests/test_conditional_multitask_cli.py
tests/test_dataset_logic.py
tests/test_e2e_foundation.py
tests/test_env_validation.py
tests/test_eval_ontology_plumbing.py
tests/test_evaluate_cli.py
tests/test_evaluate_multitask.py
tests/test_event_bounded.py
tests/test_event_bounds_oracle.py
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tests/test_feature_liveness.py
tests/test_features_e2e_cli.py
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tests/test_generate_tasks.py
tests/test_lightning_logic.py
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tests/test_multitask_ontology_targets.py
tests/test_ontology.py
tests/test_ontology_differential.py
tests/test_ontology_embedding.py
tests/test_ontology_golden.py
tests/test_predict_cli.py
tests/test_predict_logic.py
tests/test_process_data.py
tests/test_query_sequence_labeling_cli.py
tests/test_queryseq_collate.py
tests/test_queryseq_starts.py
tests/test_resumable_datamodule.py
tests/test_resume_check.py
tests/test_rope_strip_guard.py
tests/test_rope_strip_oracle.py
tests/test_rope_time.py
tests/test_sample_task_tracking_pairs_cli.py
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tests/test_task_seq_bounds.py
tests/test_train.py
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tests/test_train_hydra_dirs.py
tests/test_training.py
tests/test_window_bounds_contract.py
tests/multitask/__init__.py
tests/multitask/conftest.py
tests/multitask/test_conditional_multitask_datamodule.py
tests/multitask/test_conditional_multitask_lightning.py
tests/multitask/test_interval_table.py
tests/multitask/test_multibound_labeling.py
tests/multitask/test_multitask_orchestration.py
tests/multitask/test_predict_multitask_logic.py
tests/multitask/test_prevalence_weighting.py
tests/ontology_suite/__init__.py
tests/ontology_suite/golden.py
tests/ontology_suite/oracle.py
tests/ontology_suite/production.py
tests/sampler/__init__.py
tests/sampler/conftest.py
tests/sampler/test_eval_grid_per_shard.py
tests/sampler/test_eval_grid_starts.py
tests/sampler/test_eval_grid_support_filter.py
tests/sampler/test_orchestration.py
tests/sampler/test_pure_helpers.py
tests/sampler/test_sequence_orchestration.py
tests/sampler/test_stage0_prediction_times.py
tests/sampler/test_stage1_query_distribution.py
tests/sampler/test_stage1_sequence_distribution.py
tests/sampler/test_stage2_patient_contexts.py
tests/sampler/test_stage3_build_index.py
tests/sampler/test_stage3_sequence_index.py
tests/sampler/test_stage4_labeling.py
tests/training_validity/README.md
tests/training_validity/__init__.py
tests/training_validity/conftest.py
tests/training_validity/test_training_validity.py