LICENSE
README.md
pyproject.toml
phenome/__init__.py
phenome/_logging.py
phenome/pipeline.py
phenome/plotly_display.py
phenome/py.typed
phenome.egg-info/PKG-INFO
phenome.egg-info/SOURCES.txt
phenome.egg-info/dependency_links.txt
phenome.egg-info/entry_points.txt
phenome.egg-info/requires.txt
phenome.egg-info/top_level.txt
phenome/core/__init__.py
phenome/core/_processing_pipeline_persist.py
phenome/core/batch_correction.py
phenome/core/dataframe_contract.py
phenome/core/pipeline_results.py
phenome/core/processing_pipeline.py
phenome/core/property_utils.py
phenome/core/protocols.py
phenome/core/results_export.py
phenome/core/results_metadata.py
phenome/core/results_validation.py
phenome/core/run_log.py
phenome/core/math/__init__.py
phenome/core/math/combined_features.py
phenome/core/math/correlation.py
phenome/core/math/dimensionality_reduction.py
phenome/core/math/interpretability.py
phenome/io/__init__.py
phenome/io/_checkpoint_ops.py
phenome/io/_discovery_ops.py
phenome/io/_path_utils.py
phenome/io/batch_correction_ops.py
phenome/io/checkpoint.py
phenome/io/checkpoint_alignment.py
phenome/io/discovery.py
phenome/mcp/__init__.py
phenome/mcp/docs_search.py
phenome/mcp/recipes.py
phenome/mcp/server.py
phenome/metadata/__init__.py
phenome/metadata/base.py
phenome/metadata/sources.py
phenome/mixins/__init__.py
phenome/mixins/_helpers.py
phenome/mixins/analysis.py
phenome/mixins/batch_correction.py
phenome/mixins/dataset.py
phenome/mixins/distances.py
phenome/mixins/embedding_extractor.py
phenome/mixins/interactive/__init__.py
phenome/mixins/interactive/_html_components.py
phenome/mixins/interactive/_protocol.py
phenome/mixins/interactive/_utils.py
phenome/mixins/interactive/explorer.py
phenome/mixins/properties/__init__.py
phenome/mixins/properties/_compute.py
phenome/mixins/properties/_grouping_table.py
phenome/mixins/properties/_paths.py
phenome/mixins/properties/_report.py
phenome/mixins/properties/_workers.py
phenome/mixins/properties/grouping.py
phenome/mixins/properties/main.py
phenome/mixins/properties/matrix.py
phenome/mixins/visualization/__init__.py
phenome/mixins/visualization/_component_correlation_plots.py
phenome/mixins/visualization/_core.py
phenome/mixins/visualization/_distance_plots.py
phenome/mixins/visualization/_dr_plots.py
phenome/mixins/visualization/_group_enrichment_plots.py
phenome/mixins/visualization/_helpers.py
phenome/mixins/visualization/_image_display.py
phenome/mixins/visualization/_interpretability_plots.py
phenome/plugins/__init__.py
phenome/plugins/builtin_properties.py
phenome/plugins/registry.py
phenome/report/__init__.py
phenome/report/_components.py
phenome/report/_section_helpers.py
phenome/report/context.py
phenome/report/generator.py
phenome/report/helpers.py
phenome/report/scripts.py
phenome/report/styles.py
phenome/report/sections/__init__.py
phenome/report/sections/clustering.py
phenome/report/sections/correlation.py
phenome/report/sections/distance.py
phenome/report/sections/export.py
phenome/report/sections/gallery.py
phenome/report/sections/interpretability.py
phenome/report/sections/outlier.py
phenome/report/sections/overview.py
phenome/report/sections/property_stats.py
phenome/report/sections/run_settings.py
phenome/report/sections/visualization.py
phenome/utils/__init__.py
phenome/utils/device.py
phenome/utils/display_names.py
phenome/utils/metadata.py
phenome/utils/model_wrapper.py
phenome/utils/path_utils.py
phenome/utils/progress.py
phenome/utils/property_factories.py
phenome/utils/transforms.py
tests/test_core_smoke.py
tests/test_dependency_compat.py