LICENSE
NOTICE.md
README.md
pyproject.toml
src/phospy/__init__.py
src/phospy/_frame_ownership.py
src/phospy/cli.py
src/phospy/site_ids.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/models.py
src/phospy/activities/scoring.py
src/phospy/api/__init__.py
src/phospy/api/builders.py
src/phospy/api/datasets.py
src/phospy/api/enums.py
src/phospy/api/requests.py
src/phospy/api/results.py
src/phospy/api/workflows.py
src/phospy/api/configs/__init__.py
src/phospy/api/configs/common.py
src/phospy/api/configs/dataset.py
src/phospy/api/configs/kinase.py
src/phospy/api/configs/prediction.py
src/phospy/api/configs/preprocessing.py
src/phospy/api/configs/references.py
src/phospy/api/configs/signalome.py
src/phospy/data/reference_bundles/rat/l6_native/motif_scores.csv
src/phospy/data/reference_bundles/rat/l6_native/motif_sizes.csv
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/models.py
src/phospy/datasets/processing_state.py
src/phospy/datasets/builders/__init__.py
src/phospy/datasets/builders/contracts.py
src/phospy/datasets/builders/executor.py
src/phospy/datasets/builders/interpreter.py
src/phospy/datasets/builders/normalizer.py
src/phospy/datasets/builders/preprocessing.py
src/phospy/datasets/builders/public.py
src/phospy/datasets/builders/reader.py
src/phospy/datasets/builders/sequence_derivation.py
src/phospy/datasets/builders/transformation_resolver.py
src/phospy/datasets/builders/validator.py
src/phospy/datasets/preprocessing/__init__.py
src/phospy/datasets/preprocessing/models.py
src/phospy/datasets/preprocessing/pipeline.py
src/phospy/datasets/preprocessing/report_rows.py
src/phospy/datasets/preprocessing/report_schema.py
src/phospy/datasets/preprocessing/stages/__init__.py
src/phospy/datasets/preprocessing/stages/comparisons.py
src/phospy/datasets/preprocessing/stages/intensity_transform.py
src/phospy/datasets/preprocessing/stages/missing_data.py
src/phospy/datasets/preprocessing/stages/normalisation.py
src/phospy/datasets/preprocessing/stages/site_matrix.py
src/phospy/datasets/preprocessing/stages/site_matrix_components.py
src/phospy/datasets/preprocessing/stages/total_protein_correction.py
src/phospy/errors/__init__.py
src/phospy/errors/base.py
src/phospy/errors/build.py
src/phospy/errors/input.py
src/phospy/errors/references.py
src/phospy/errors/transformations.py
src/phospy/errors/validation.py
src/phospy/errors/workflows.py
src/phospy/io/__init__.py
src/phospy/io/cli.py
src/phospy/io/bundles/__init__.py
src/phospy/io/bundles/kinase.py
src/phospy/io/bundles/signalome.py
src/phospy/io/bundles/_kinase/__init__.py
src/phospy/io/bundles/_kinase/constants.py
src/phospy/io/bundles/_kinase/loader.py
src/phospy/io/bundles/_kinase/manifest.py
src/phospy/io/bundles/_kinase/models.py
src/phospy/io/bundles/_kinase/reconstruction.py
src/phospy/io/bundles/_kinase/snapshots.py
src/phospy/io/bundles/_kinase/writer.py
src/phospy/io/bundles/_shared/__init__.py
src/phospy/io/bundles/_shared/intensity_scale_state.py
src/phospy/io/bundles/_shared/json_files.py
src/phospy/io/bundles/_shared/organisms.py
src/phospy/io/bundles/_shared/paths.py
src/phospy/io/bundles/_shared/primitives.py
src/phospy/io/bundles/_shared/processing_state.py
src/phospy/io/bundles/_shared/tables.py
src/phospy/io/bundles/_signalome/__init__.py
src/phospy/io/bundles/_signalome/compatibility.py
src/phospy/io/bundles/_signalome/constants.py
src/phospy/io/bundles/_signalome/loader.py
src/phospy/io/bundles/_signalome/manifest.py
src/phospy/io/bundles/_signalome/models.py
src/phospy/io/bundles/_signalome/reconstruction.py
src/phospy/io/bundles/_signalome/snapshots.py
src/phospy/io/bundles/_signalome/writer.py
src/phospy/io/publishers/__init__.py
src/phospy/io/publishers/workflows.py
src/phospy/io/readers/__init__.py
src/phospy/io/readers/tables.py
src/phospy/prediction/__init__.py
src/phospy/prediction/candidates.py
src/phospy/prediction/execution.py
src/phospy/prediction/models.py
src/phospy/prediction/motif_scoring.py
src/phospy/prediction/policies.py
src/phospy/prediction/sampling_core.py
src/phospy/prediction/sampling_runtime.py
src/phospy/prediction/scoring.py
src/phospy/prediction/sequence_validation.py
src/phospy/prediction/svm.py
src/phospy/provenance/__init__.py
src/phospy/provenance/environment.py
src/phospy/provenance/hashing.py
src/phospy/provenance/models.py
src/phospy/provenance/serialization.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/assignments.py
src/phospy/signalomes/constants.py
src/phospy/signalomes/context.py
src/phospy/signalomes/expanded.py
src/phospy/signalomes/models.py
src/phospy/signalomes/modules.py
src/phospy/signalomes/network.py
src/phospy/signalomes/science.py
src/phospy/signalomes/clustering/__init__.py
src/phospy/signalomes/clustering/backend_dispatch.py
src/phospy/signalomes/clustering/contracts.py
src/phospy/signalomes/clustering/diagnostics.py
src/phospy/signalomes/clustering/exact_python.py
src/phospy/signalomes/clustering/models.py
src/phospy/signalomes/clustering/orchestration.py
src/phospy/signalomes/clustering/protocol.py
src/phospy/signalomes/clustering/scipy_hierarchical.py
src/phospy/signalomes/clustering/selection.py
src/phospy/signalomes/clustering/validation.py
src/phospy/signalomes/clustering/backends/__init__.py
src/phospy/signalomes/clustering/backends/exact_python.py
src/phospy/signalomes/clustering/backends/scipy_hierarchical.py
src/phospy/tables/__init__.py
src/phospy/tables/activity.py
src/phospy/tables/base.py
src/phospy/tables/datasets.py
src/phospy/tables/kinase.py
src/phospy/tables/references.py
src/phospy/tables/signalome.py
src/phospy/transformations/__init__.py
src/phospy/transformations/_authority.py
src/phospy/transformations/contracts.py
src/phospy/transformations/models.py
src/phospy/transformations/transformers/__init__.py
src/phospy/transformations/transformers/identity.py
src/phospy/validation/__init__.py
src/phospy/validation/ownership.py
src/phospy/validation/common/__init__.py
src/phospy/validation/common/dataframes.py
src/phospy/validation/common/missing_values.py
src/phospy/validation/common/numbers.py
src/phospy/validation/common/numeric_frames.py
src/phospy/validation/datasets/__init__.py
src/phospy/validation/datasets/analysis_ready.py
src/phospy/validation/datasets/inputs.py
src/phospy/validation/datasets/preprocessing.py
src/phospy/validation/references/__init__.py
src/phospy/validation/references/bundle.py
src/phospy/validation/references/compatibility.py
src/phospy/validation/transformations/__init__.py
src/phospy/validation/transformations/state.py
src/phospy/validation/workflows/__init__.py
src/phospy/validation/workflows/activity.py
src/phospy/validation/workflows/configs.py
src/phospy/workflows/__init__.py
src/phospy/workflows/kinase/__init__.py
src/phospy/workflows/kinase/contracts.py
src/phospy/workflows/kinase/executor.py
src/phospy/workflows/kinase/interpreter.py
src/phospy/workflows/kinase/public.py
src/phospy/workflows/kinase/science.py
src/phospy/workflows/kinase/validator.py
src/phospy/workflows/signalome/__init__.py
src/phospy/workflows/signalome/clustering_runner.py
src/phospy/workflows/signalome/component_helpers.py
src/phospy/workflows/signalome/component_models.py
src/phospy/workflows/signalome/components.py
src/phospy/workflows/signalome/constants.py
src/phospy/workflows/signalome/context_tables.py
src/phospy/workflows/signalome/contracts.py
src/phospy/workflows/signalome/executor.py
src/phospy/workflows/signalome/interpreter.py
src/phospy/workflows/signalome/module_tables.py
src/phospy/workflows/signalome/network_builder.py
src/phospy/workflows/signalome/provenance.py
src/phospy/workflows/signalome/public.py
src/phospy/workflows/signalome/result_assembly.py
src/phospy/workflows/signalome/validator.py