LICENSE
README.md
pyproject.toml
ANDREA.egg-info/PKG-INFO
ANDREA.egg-info/SOURCES.txt
ANDREA.egg-info/dependency_links.txt
ANDREA.egg-info/entry_points.txt
ANDREA.egg-info/requires.txt
ANDREA.egg-info/top_level.txt
andrea/__init__.py
andrea/__main__.py
andrea/config.py
andrea/catalog_inference_tools/__init__.py
andrea/catalog_inference_tools/input_specs/cell_cell_interactions.json
andrea/catalog_inference_tools/input_specs/chromatin_accessibility.json
andrea/catalog_inference_tools/input_specs/chromatin_regions.json
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andrea/catalog_inference_tools/input_specs/cluster_markers.json
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andrea/catalog_inference_tools/input_specs/column_phenotypes.json
andrea/catalog_inference_tools/input_specs/enrichment_background.json
andrea/catalog_inference_tools/input_specs/expression_matrix.json
andrea/catalog_inference_tools/input_specs/grnboost_network.json
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andrea/catalog_inference_tools/input_specs/interventions.json
andrea/catalog_inference_tools/input_specs/lineage_tree.json
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andrea/catalog_inference_tools/tools/ppcor/cost.json
andrea/catalog_inference_tools/tools/ppcor/toolspec.json
andrea/catalog_inference_tools/tools/pyscenic/cost.json
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andrea/catalog_inference_tools/tools/scgenerai/cost.json
andrea/catalog_inference_tools/tools/scgenerai/toolspec.json
andrea/catalog_inference_tools/tools/scing/cost.json
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andrea/catalog_inference_tools/tools/scminer/cost.json
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andrea/catalog_inference_tools/tools/scmtni/toolspec.json
andrea/catalog_inference_tools/tools/scregulate/cost.json
andrea/catalog_inference_tools/tools/scregulate/toolspec.json
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andrea/catalog_inference_tools/tools/simic/cost.json
andrea/catalog_inference_tools/tools/simic/toolspec.json
andrea/catalog_inference_tools/tools/tigress/cost.json
andrea/catalog_inference_tools/tools/tigress/toolspec.json
andrea/catalog_simulation_data_tools/__init__.py
andrea/catalog_simulation_data_tools/input_specs/boolode_boolean_model.json
andrea/catalog_simulation_data_tools/input_specs/boolode_initial_conditions.json
andrea/catalog_simulation_data_tools/input_specs/boolode_interaction_strengths.json
andrea/catalog_simulation_data_tools/input_specs/gnw_dynamical_network.json
andrea/catalog_simulation_data_tools/input_specs/groundgan_causal_controller_checkpoint.json
andrea/catalog_simulation_data_tools/input_specs/groundgan_causal_graph_pickle.json
andrea/catalog_simulation_data_tools/input_specs/groundgan_model_checkpoint.json
andrea/catalog_simulation_data_tools/input_specs/groundgan_reference_h5ad.json
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andrea/catalog_simulation_data_tools/schemas/ground-truth-manifest.schema.json
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andrea/catalog_simulation_data_tools/simulators/dyngen/cost.json
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andrea/catalog_simulation_data_tools/simulators/genespider2/cost.json
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andrea/catalog_simulation_data_tools/simulators/groundgan/cost.json
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andrea/catalog_simulation_data_tools/simulators/scmultisim/cost.json
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andrea/catalog_simulation_data_tools/simulators/syntren/cost.json
andrea/catalog_simulation_data_tools/simulators/syntren/simulatorspec.json
andrea/cli/__init__.py
andrea/cli/app.py
andrea/core/__init__.py
andrea/core/commands/__init__.py
andrea/core/commands/compare_networks/__init__.py
andrea/core/commands/compare_networks/bundles.py
andrea/core/commands/compare_networks/comparison.py
andrea/core/commands/compare_networks/distances.py
andrea/core/commands/compare_networks/loading.py
andrea/core/commands/compare_networks/models.py
andrea/core/commands/compare_networks/request.py
andrea/core/commands/compare_networks/store.py
andrea/core/commands/compare_networks/tables.py
andrea/core/commands/compare_networks/utils.py
andrea/core/commands/compare_networks/view.py
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andrea/core/commands/compare_networks/view_assets/view.css
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andrea/core/commands/evaluate_inference/__init__.py
andrea/core/commands/evaluate_inference/bundles.py
andrea/core/commands/evaluate_inference/evaluation.py
andrea/core/commands/evaluate_inference/view_assets/__init__.py
andrea/core/commands/evaluate_inference/view_assets/template.html
andrea/core/commands/evaluate_inference/view_assets/view.css
andrea/core/commands/evaluate_inference/view_assets/view.js
andrea/core/commands/generate_data/__init__.py
andrea/core/commands/generate_data/bootstrap.py
andrea/core/commands/generate_data/bundles.py
andrea/core/commands/generate_data/catalog.py
andrea/core/commands/generate_data/cost_planner.py
andrea/core/commands/generate_data/output_validation.py
andrea/core/commands/generate_data/pipeline.py
andrea/core/commands/generate_data/plan.py
andrea/core/commands/generate_data/request.py
andrea/core/commands/generate_data/scenario.py
andrea/core/commands/generate_data/selection.py
andrea/core/commands/generate_data/semantic.py
andrea/core/commands/generate_data/shared.py
andrea/core/commands/generate_data/backends/__init__.py
andrea/core/commands/generate_data/backends/docker_runner.py
andrea/core/commands/generate_data/backends/registry.py
andrea/core/commands/infer_network/__init__.py
andrea/core/commands/infer_network/bundles.py
andrea/core/commands/infer_network/pipeline.py
andrea/core/commands/infer_network/plan.py
andrea/core/commands/infer_network/preflight.py
andrea/core/commands/infer_network/run.py
andrea/core/commands/infer_network/commons/__init__.py
andrea/core/commands/infer_network/commons/artifacts.py
andrea/core/commands/infer_network/commons/catalog.py
andrea/core/commands/infer_network/commons/custom_tools.py
andrea/core/commands/infer_network/commons/dataset.py
andrea/core/commands/infer_network/commons/execution_state.py
andrea/core/commands/infer_network/commons/merge.py
andrea/core/commands/infer_network/commons/network_exports.py
andrea/core/commands/infer_network/commons/planner.py
andrea/core/commands/infer_network/commons/runtime_helpers.py
andrea/core/commands/infer_network/commons/shared.py
andrea/core/commands/infer_network/commons/threading.py
andrea/core/commands/infer_network/commons/tool_rule_eval.py
andrea/core/commands/infer_network/commons/tools.py
andrea/core/shared/__init__.py
andrea/core/shared/bundles.py
andrea/core/shared/catalog_contracts.py
andrea/core/shared/compatibility_rules.py
andrea/core/shared/container_runtime.py
andrea/core/shared/input_specs.py
andrea/core/shared/input_validation.py
andrea/core/shared/issues.py
andrea/core/shared/json_io.py
andrea/core/shared/network_context.py
andrea/core/shared/param_validation.py
andrea/core/shared/paths.py
andrea/core/shared/progress.py
andrea/core/shared/runtime_profile.py
andrea/gui/__init__.py
andrea/gui/common/__init__.py
andrea/gui/common/reproducibility.py
andrea/gui/common/server_files.py
andrea/gui/common/server_jobs.py
andrea/gui/common/static/app/network_context.js
andrea/gui/common/static/app/bundles/modal.js
andrea/gui/common/static/app/bundles/styles.css
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andrea/gui/common/static/app/core/dom.js
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andrea/gui/common/static/app/uploads/progress.js
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andrea/gui/compare_networks/__init__.py
andrea/gui/compare_networks/server.py
andrea/gui/compare_networks/static/index.html
andrea/gui/compare_networks/static/styles.css
andrea/gui/compare_networks/static/app/main.js
andrea/gui/compare_networks/static/app/shared.js
andrea/gui/evaluate_inference/__init__.py
andrea/gui/evaluate_inference/server.py
andrea/gui/evaluate_inference/static/index.html
andrea/gui/evaluate_inference/static/styles.css
andrea/gui/evaluate_inference/static/app/main.js
andrea/gui/generate_data/__init__.py
andrea/gui/generate_data/server.py
andrea/gui/generate_data/static/index.html
andrea/gui/generate_data/static/styles.css
andrea/gui/generate_data/static/app/execution_view.js
andrea/gui/generate_data/static/app/main.js
andrea/gui/generate_data/static/app/plan_view.js
andrea/gui/generate_data/static/app/preflight_view.js
andrea/gui/generate_data/static/app/runs.js
andrea/gui/generate_data/static/app/scenario_templates.js
andrea/gui/generate_data/static/app/simulator_catalog.js
andrea/gui/infer_network/__init__.py
andrea/gui/infer_network/server.py
andrea/gui/infer_network/static/index.html
andrea/gui/infer_network/static/styles.css
andrea/gui/infer_network/static/app/main.js
andrea/gui/infer_network/static/app/catalog/external_tools.js
andrea/gui/infer_network/static/app/catalog/model.js
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andrea/gui/infer_network/static/app/core/api.js
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andrea/gui/infer_network/static/app/dataset/expression.js
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andrea/gui/infer_network/static/app/files/explorer.js
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andrea/gui/infer_network/static/app/runs/params_modal.js
andrea/gui/infer_network/static/app/runtime/view.js
andrea/gui/infer_network/static/app/ui/popovers.js
andrea/gui/infer_network/static/app/ui/steps.js
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tests/test_cli_bootstrap.py