LICENSE
NOTICE.md
README.md
pyproject.toml
src/phospy/__init__.py
src/phospy/cli.py
src/phospy.egg-info/PKG-INFO
src/phospy.egg-info/SOURCES.txt
src/phospy.egg-info/dependency_links.txt
src/phospy.egg-info/entry_points.txt
src/phospy.egg-info/requires.txt
src/phospy.egg-info/top_level.txt
src/phospy/activities/__init__.py
src/phospy/activities/analysis.py
src/phospy/activities/results.py
src/phospy/activities/scoring.py
src/phospy/api/__init__.py
src/phospy/api/contracts.py
src/phospy/api/orchestration.py
src/phospy/api/signalome_workflows.py
src/phospy/api/simple_workflows.py
src/phospy/api/workflow_results.py
src/phospy/data/reference_bundles/rat/l6_native/site_sequences.csv
src/phospy/data/reference_bundles/rat/l6_native/substrate_map.csv
src/phospy/datasets/__init__.py
src/phospy/datasets/builders.py
src/phospy/datasets/loaders.py
src/phospy/datasets/models.py
src/phospy/datasets/schema.py
src/phospy/errors/__init__.py
src/phospy/errors/base.py
src/phospy/errors/validation.py
src/phospy/internal/__init__.py
src/phospy/internal/constants.py
src/phospy/internal/defaults.py
src/phospy/internal/kinase_workflows.py
src/phospy/internal/pipeline.py
src/phospy/internal/types.py
src/phospy/io/__init__.py
src/phospy/io/mappings.py
src/phospy/io/publishing.py
src/phospy/io/readers.py
src/phospy/io/writers.py
src/phospy/prediction/__init__.py
src/phospy/prediction/aggregation.py
src/phospy/prediction/candidates.py
src/phospy/prediction/contracts.py
src/phospy/prediction/engines.py
src/phospy/prediction/execution.py
src/phospy/prediction/motif_scoring.py
src/phospy/prediction/policies.py
src/phospy/prediction/profiles.py
src/phospy/prediction/results.py
src/phospy/prediction/sampling.py
src/phospy/prediction/sampling_core.py
src/phospy/prediction/sampling_runtime.py
src/phospy/prediction/sampling_trace_writer.py
src/phospy/prediction/scoring.py
src/phospy/prediction/svm.py
src/phospy/prediction/trace_export.py
src/phospy/prediction/trace_replay.py
src/phospy/prediction/trace_runtime.py
src/phospy/prediction/traces.py
src/phospy/prediction/validation.py
src/phospy/preprocessing/__init__.py
src/phospy/preprocessing/analysis_ready.py
src/phospy/preprocessing/core.py
src/phospy/preprocessing/dataset.py
src/phospy/preprocessing/matrices.py
src/phospy/preprocessing/modes.py
src/phospy/preprocessing/primitives.py
src/phospy/preprocessing/protein_correction.py
src/phospy/preprocessing/services.py
src/phospy/preprocessing/site_matrix.py
src/phospy/preprocessing/steps.py
src/phospy/references/__init__.py
src/phospy/references/models.py
src/phospy/references/resolution.py
src/phospy/references/resources.py
src/phospy/signalomes/__init__.py
src/phospy/signalomes/analysis.py
src/phospy/signalomes/assignments.py
src/phospy/signalomes/clustering.py
src/phospy/signalomes/constants.py
src/phospy/signalomes/maps.py
src/phospy/signalomes/networks.py
src/phospy/signalomes/results.py
src/phospy/signalomes/serialization.py
src/phospy/signalomes/site_ids.py
src/phospy/validation/__init__.py
src/phospy/validation/compatibility/__init__.py
src/phospy/validation/compatibility/matrices.py
src/phospy/validation/compatibility/proteins.py
src/phospy/validation/domain/__init__.py
src/phospy/validation/domain/comparisons.py
src/phospy/validation/domain/prediction.py
src/phospy/validation/domain/references.py
src/phospy/validation/domain/signalomes.py
src/phospy/validation/requests/__init__.py
src/phospy/validation/requests/analysis.py
src/phospy/validation/requests/dataset.py
src/phospy/validation/requests/pipeline.py
src/phospy/validation/requests/prediction.py
src/phospy/validation/requests/signalome.py
src/phospy/validation/requests/workflow.py
src/phospy/validation/schema/__init__.py
src/phospy/validation/schema/files.py
src/phospy/validation/schema/frames.py
src/phospy/validation/schema/tables.py
src/phospy/validation/values/__init__.py
src/phospy/validation/values/collections.py
src/phospy/validation/values/enums.py
src/phospy/validation/values/identifiers.py
src/phospy/validation/values/numeric.py
tests/test_activities.py
tests/test_activities_package_structure.py
tests/test_analysis.py
tests/test_api.py
tests/test_api_orchestration_regression.py
tests/test_architecture_docs.py
tests/test_cli_smoke.py
tests/test_dataset_schema.py
tests/test_datasets_package.py
tests/test_domain_package_skeleton.py
tests/test_domain_validation_errors.py
tests/test_end_to_end_parity.py
tests/test_fragile_support_reference.py
tests/test_import_migration_audit.py
tests/test_matrices.py
tests/test_motifs.py
tests/test_parity-with_metrics.py
tests/test_parity.py
tests/test_pipeline_publishing.py
tests/test_prediction.py
tests/test_prediction_components.py
tests/test_prediction_package_structure.py
tests/test_preprocessing.py
tests/test_preprocessing_package_structure.py
tests/test_profiles.py
tests/test_public_api.py
tests/test_readme_smoke.py
tests/test_reference_workflow_seams.py
tests/test_references_package_structure.py
tests/test_scoring.py
tests/test_signalome_maps.py
tests/test_signalome_networks.py
tests/test_signalomes.py
tests/test_signalomes_package_structure.py
tests/test_support_packages_structure.py
tests/test_validation_compatibility.py
tests/test_validation_paths.py
tests/test_validation_requests.py
tests/test_validation_tables.py
tests/test_validation_type_modules.py
tests/test_workflow.py