CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
.claude/README.md
.claude/settings.json
.claude/settings.local.json
.claude/commands/clean.md
.claude/commands/lint.md
.claude/commands/sage.md
.claude/commands/test.md
.claude/scripts/check-build-drift.sh
.claude/scripts/clean-artifacts.sh
.claude/scripts/run-tests.sh
.claude/skills/sage-cli/SKILL.md
.claude/skills/sage-lib-analysis/SKILL.md
.claude/skills/sage-lib-best-practices/SKILL.md
.claude/skills/sage-lib-geometry-analysis/SKILL.md
.claude/skills/sage-lib-input-files/SKILL.md
.claude/skills/sage-lib-io/SKILL.md
.claude/skills/sage-lib-partitions/SKILL.md
.claude/skills/sage-lib-singlerun/SKILL.md
.claude/skills/sage-lib-storage/SKILL.md
.claude/skills/sage-lib-structure-building/SKILL.md
.claude/skills/sage-lib-structure-editing/SKILL.md
.claude/skills/sage-mcp/SKILL.md
.claude/workflows/sage-test-authoring.js
src/sage_lib/__init__.py
src/sage_lib/agent_diagnostics.py
src/sage_lib/agent_environment.py
src/sage_lib/agent_setup.py
src/sage_lib/claude_setup.py
src/sage_lib/main.py
src/sage_lib.egg-info/PKG-INFO
src/sage_lib.egg-info/SOURCES.txt
src/sage_lib.egg-info/dependency_links.txt
src/sage_lib.egg-info/entry_points.txt
src/sage_lib.egg-info/requires.txt
src/sage_lib.egg-info/top_level.txt
src/sage_lib/IO/BashScriptManager.py
src/sage_lib/IO/BinaryDataHandler.py
src/sage_lib/IO/ChargeFileManager.py
src/sage_lib/IO/DOSManager.py
src/sage_lib/IO/EigenvalueFileManager.py
src/sage_lib/IO/ForceFieldManager.py
src/sage_lib/IO/KPointsManager.py
src/sage_lib/IO/OutFileManager.py
src/sage_lib/IO/PROFileManager.py
src/sage_lib/IO/PotentialManager.py
src/sage_lib/IO/WaveFileManager.py
src/sage_lib/IO/__init__.py
src/sage_lib/IO/hybrid_db_remove.py
src/sage_lib/IO/input_handling_tools/InputAIMS.py
src/sage_lib/IO/input_handling_tools/InputClassic.py
src/sage_lib/IO/input_handling_tools/InputDFT.py
src/sage_lib/IO/input_handling_tools/InputDFTB.py
src/sage_lib/IO/input_handling_tools/InputFile.py
src/sage_lib/IO/input_handling_tools/InputFileManager.py
src/sage_lib/IO/input_handling_tools/__init__.py
src/sage_lib/IO/storage/__init__.py
src/sage_lib/IO/storage/backend.py
src/sage_lib/IO/storage/composite.py
src/sage_lib/IO/storage/hybrid.py
src/sage_lib/IO/storage/maintenance.py
src/sage_lib/IO/storage/memory.py
src/sage_lib/IO/storage/remote.py
src/sage_lib/IO/storage/sqlite.py
src/sage_lib/IO/storage/tools.py
src/sage_lib/IO/structure_handling_tools/AtomPosition.py
src/sage_lib/IO/structure_handling_tools/AtomPositionLoader.py
src/sage_lib/IO/structure_handling_tools/AtomPositionMaker.py
src/sage_lib/IO/structure_handling_tools/AtomPositionManager.py
src/sage_lib/IO/structure_handling_tools/AtomPositionOperator.py
src/sage_lib/IO/structure_handling_tools/NonPeriodicSystem.py
src/sage_lib/IO/structure_handling_tools/PeriodicSystem.py
src/sage_lib/IO/structure_handling_tools/__init__.py
src/sage_lib/IO/structure_handling_tools/oxide_surfaces.py
src/sage_lib/IO/structure_handling_tools/plot.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/AIMS.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/ASE.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/CIF.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/DCD.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/DUMP.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/GAUSSIAN.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/GEN.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/LAMMPS.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/PDB.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/POSCAR.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/PSF.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/SI.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/XYZ.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/__init__.py
src/sage_lib/IO/structure_handling_tools/structural_file_readers/gaussian_normal_modes.py
src/sage_lib/agent_assets/__init__.py
src/sage_lib/agent_assets/commands/sage.md
src/sage_lib/agent_assets/examples/h2.xyz
src/sage_lib/agent_assets/skills/sage-cli/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-analysis/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-best-practices/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-geometry-analysis/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-input-files/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-io/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-partitions/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-singlerun/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-storage/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-structure-building/SKILL.md
src/sage_lib/agent_assets/skills/sage-lib-structure-editing/SKILL.md
src/sage_lib/agent_assets/skills/sage-mcp/SKILL.md
src/sage_lib/descriptor/MBTR.py
src/sage_lib/descriptor/MDTR_rev.py
src/sage_lib/descriptor/__init__.py
src/sage_lib/ensemble/Ensemble.py
src/sage_lib/ensemble/__init__.py
src/sage_lib/master/AtomicProperties.py
src/sage_lib/master/FileManager.py
src/sage_lib/master/__init__.py
src/sage_lib/mcp/__init__.py
src/sage_lib/mcp/__main__.py
src/sage_lib/mcp/edits.py
src/sage_lib/mcp/gui.py
src/sage_lib/mcp/server.py
src/sage_lib/mcp/tools.py
src/sage_lib/mcp/workspace.py
src/sage_lib/miscellaneous/BandPathGenerator.py
src/sage_lib/miscellaneous/MD_tools.py
src/sage_lib/miscellaneous/SOAP.py
src/sage_lib/miscellaneous/SOAP_tools.py
src/sage_lib/miscellaneous/__init__.py
src/sage_lib/miscellaneous/data_mining.py
src/sage_lib/miscellaneous/fibonacci_surface.py
src/sage_lib/miscellaneous/get_bravais_lattice.py
src/sage_lib/miscellaneous/marching_cubes.py
src/sage_lib/miscellaneous/math_tools.py
src/sage_lib/miscellaneous/periodic_kdtree.py
src/sage_lib/miscellaneous/periodic_kdtree_C.py
src/sage_lib/miscellaneous/periodic_kdtree_legacy.py
src/sage_lib/miscellaneous/potentials.py
src/sage_lib/miscellaneous/surface_sampling.py
src/sage_lib/miscellaneous/hdbscan/__init__.py
src/sage_lib/miscellaneous/hdbscan/branches.py
src/sage_lib/miscellaneous/hdbscan/flat.py
src/sage_lib/miscellaneous/hdbscan/hdbscan_.py
src/sage_lib/miscellaneous/hdbscan/plots.py
src/sage_lib/miscellaneous/hdbscan/prediction.py
src/sage_lib/miscellaneous/hdbscan/robust_single_linkage_.py
src/sage_lib/miscellaneous/hdbscan/validity.py
src/sage_lib/miscellaneous/hdbscan/tests/__init__.py
src/sage_lib/miscellaneous/hdbscan/tests/test_branches.py
src/sage_lib/miscellaneous/hdbscan/tests/test_flat.py
src/sage_lib/miscellaneous/hdbscan/tests/test_hdbscan.py
src/sage_lib/miscellaneous/hdbscan/tests/test_prediction_utils.py
src/sage_lib/miscellaneous/hdbscan/tests/test_rsl.py
src/sage_lib/partition/Partition.py
src/sage_lib/partition/PartitionManager.py
src/sage_lib/partition/__init__.py
src/sage_lib/partition/partition_analysis/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/electrochemical.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/feature_analysis.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/feature_explanation.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/feature_reduction.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/model_evaluation.py
src/sage_lib/partition/partition_analysis/featurizer/analysis/xgb_postanalysis.py
src/sage_lib/partition/partition_analysis/featurizer/core/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/core/featurizer.py
src/sage_lib/partition/partition_analysis/featurizer/core/graph_builder.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/chemistry.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/correlation.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/order.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/percolation.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/spectral.py
src/sage_lib/partition/partition_analysis/featurizer/core/descriptors/topology.py
src/sage_lib/partition/partition_analysis/featurizer/examples/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/examples/demo_chemical_analysis.py
src/sage_lib/partition/partition_analysis/featurizer/examples/demo_general_analysis.py
src/sage_lib/partition/partition_analysis/featurizer/examples/simple_extractor.py
src/sage_lib/partition/partition_analysis/featurizer/tests/__init__.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_descriptors.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_discriminative.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_electrochemical.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_explanation.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_feature_reduction.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_feature_reduction_handles.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_featurizer.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_featurizer_vib.py
src/sage_lib/partition/partition_analysis/featurizer/tests/test_graph.py
src/sage_lib/partition/partition_builder/AbInitioThermodynamics_builder.py
src/sage_lib/partition/partition_builder/BandStructure_builder.py
src/sage_lib/partition/partition_builder/BasePartition.py
src/sage_lib/partition/partition_builder/Blender_builder.py
src/sage_lib/partition/partition_builder/Conductivity_builder.py
src/sage_lib/partition/partition_builder/Config_builder.py
src/sage_lib/partition/partition_builder/CrystalDefect_builder.py
src/sage_lib/partition/partition_builder/Crystal_builder.py
src/sage_lib/partition/partition_builder/Extract_builder.py
src/sage_lib/partition/partition_builder/Filter_builder.py
src/sage_lib/partition/partition_builder/Metadata_builder.py
src/sage_lib/partition/partition_builder/MolecularDynamic_builder.py
src/sage_lib/partition/partition_builder/MoleculeCluster_builder.py
src/sage_lib/partition/partition_builder/Molecule_builder.py
src/sage_lib/partition/partition_builder/Network_builder.py
src/sage_lib/partition/partition_builder/Plot_builder.py
src/sage_lib/partition/partition_builder/PositionEditor_builder.py
src/sage_lib/partition/partition_builder/SurfaceStates_builder.py
src/sage_lib/partition/partition_builder/VacuumStates_builder.py
src/sage_lib/partition/partition_builder/__init__.py
src/sage_lib/single_run/FF_Gap.py
src/sage_lib/single_run/SingleRun.py
src/sage_lib/single_run/SingleRunDFT.py
src/sage_lib/single_run/SingleRunManager.py
src/sage_lib/single_run/__init__.py
src/sage_lib/visualization/PartitionProvider.py
src/sage_lib/visualization/RemotePartitionProvider.py
src/sage_lib/visualization/__init__.py
src/sage_lib/visualization/_viz_shared.py
src/sage_lib/visualization/assistant_capabilities.py
src/sage_lib/visualization/assistant_database.py
src/sage_lib/visualization/assistant_ensemble.py
src/sage_lib/visualization/assistant_filter.py
src/sage_lib/visualization/assistant_motifs.py
src/sage_lib/visualization/assistant_query.py
src/sage_lib/visualization/assistant_scene_models.py
src/sage_lib/visualization/assistant_session.py
src/sage_lib/visualization/assistant_simulation.py
src/sage_lib/visualization/assistant_versions.py
src/sage_lib/visualization/browser.py
src/sage_lib/visualization/camera.py
src/sage_lib/visualization/capture.py
src/sage_lib/visualization/constants.py
src/sage_lib/visualization/imgui_compat.py
src/sage_lib/visualization/keyframe_studio.py
src/sage_lib/visualization/mcp_bridge.py
src/sage_lib/visualization/model_catalogue.py
src/sage_lib/visualization/model_materials.py
src/sage_lib/visualization/model_recommendations.py
src/sage_lib/visualization/multiview.py
src/sage_lib/visualization/remote_launcher.py
src/sage_lib/visualization/scene.py
src/sage_lib/visualization/scene_models.py
src/sage_lib/visualization/visualizer.py
src/sage_lib/visualization/workspace_layout.py
src/sage_lib/visualization/analysis/__init__.py
src/sage_lib/visualization/analysis/analysis_manager.py
src/sage_lib/visualization/analysis/bond_graph.py
src/sage_lib/visualization/analysis/camera_path.py
src/sage_lib/visualization/analysis/clash_detection.py
src/sage_lib/visualization/analysis/clusters.py
src/sage_lib/visualization/analysis/comparison.py
src/sage_lib/visualization/analysis/coordination.py
src/sage_lib/visualization/analysis/disk_cache.py
src/sage_lib/visualization/analysis/displacement.py
src/sage_lib/visualization/analysis/distributions.py
src/sage_lib/visualization/analysis/ensemble_bonds.py
src/sage_lib/visualization/analysis/ensemble_cache.py
src/sage_lib/visualization/analysis/ensemble_cluster_geometry.py
src/sage_lib/visualization/analysis/ensemble_clustering.py
src/sage_lib/visualization/analysis/ensemble_composition.py
src/sage_lib/visualization/analysis/ensemble_embedding.py
src/sage_lib/visualization/analysis/ensemble_hover_info.py
src/sage_lib/visualization/analysis/ensemble_named_selections.py
src/sage_lib/visualization/analysis/ensemble_stats.py
src/sage_lib/visualization/analysis/export_engine.py
src/sage_lib/visualization/analysis/geometry.py
src/sage_lib/visualization/analysis/geometry_cache.py
src/sage_lib/visualization/analysis/hbonds.py
src/sage_lib/visualization/analysis/interactions.py
src/sage_lib/visualization/analysis/manager.py
src/sage_lib/visualization/analysis/measurement_tools.py
src/sage_lib/visualization/analysis/msd.py
src/sage_lib/visualization/analysis/mutation_engine.py
src/sage_lib/visualization/analysis/neighbor_engine.py
src/sage_lib/visualization/analysis/normal_modes.py
src/sage_lib/visualization/analysis/order_params.py
src/sage_lib/visualization/analysis/pes.py
src/sage_lib/visualization/analysis/pes_grand.py
src/sage_lib/visualization/analysis/pes_landscape.py
src/sage_lib/visualization/analysis/pes_motifs.py
src/sage_lib/visualization/analysis/polyhedron.py
src/sage_lib/visualization/analysis/polyhedron_analyzer.py
src/sage_lib/visualization/analysis/property_registry.py
src/sage_lib/visualization/analysis/protein_geometry.py
src/sage_lib/visualization/analysis/rdf.py
src/sage_lib/visualization/analysis/rotamer_templates.py
src/sage_lib/visualization/analysis/sasa.py
src/sage_lib/visualization/analysis/selection_query.py
src/sage_lib/visualization/analysis/soap_analysis.py
src/sage_lib/visualization/analysis/strain.py
src/sage_lib/visualization/analysis/tb_visualization.py
src/sage_lib/visualization/analysis/tight_binding.py
src/sage_lib/visualization/analysis/vector_field.py
src/sage_lib/visualization/analysis/vibrational_analysis.py
src/sage_lib/visualization/analysis/volumetric.py
src/sage_lib/visualization/analysis/voronoi.py
src/sage_lib/visualization/analysis/z_profile.py
src/sage_lib/visualization/avatar/__init__.py
src/sage_lib/visualization/avatar/anchors.py
src/sage_lib/visualization/avatar/controller.py
src/sage_lib/visualization/avatar/data_scout.py
src/sage_lib/visualization/avatar/draw.py
src/sage_lib/visualization/avatar/expressions.py
src/sage_lib/visualization/avatar/face.py
src/sage_lib/visualization/avatar/guess.py
src/sage_lib/visualization/avatar/llm.py
src/sage_lib/visualization/avatar/model.py
src/sage_lib/visualization/avatar/motion.py
src/sage_lib/visualization/avatar/panel.py
src/sage_lib/visualization/avatar/phrases.py
src/sage_lib/visualization/avatar/reactions.py
src/sage_lib/visualization/avatar/settings.py
src/sage_lib/visualization/avatar/social.py
src/sage_lib/visualization/avatar/strings.py
src/sage_lib/visualization/avatar/structure_kind.py
src/sage_lib/visualization/avatar/targets.py
src/sage_lib/visualization/avatar/textutil.py
src/sage_lib/visualization/avatar/tips.py
src/sage_lib/visualization/avatar/touring.py
src/sage_lib/visualization/avatar/tours.py
src/sage_lib/visualization/builder/__init__.py
src/sage_lib/visualization/builder/chemistry_rules.py
src/sage_lib/visualization/builder/edit_commands.py
src/sage_lib/visualization/builder/editor.py
src/sage_lib/visualization/builder/fragments.py
src/sage_lib/visualization/builder/id_manager.py
src/sage_lib/visualization/builder/placement_engine.py
src/sage_lib/visualization/builder/relaxation_engine.py
src/sage_lib/visualization/builder/session.py
src/sage_lib/visualization/builder/validation.py
src/sage_lib/visualization/display/__init__.py
src/sage_lib/visualization/display/annotation_drag.py
src/sage_lib/visualization/display/atom_visuals.py
src/sage_lib/visualization/display/caching.py
src/sage_lib/visualization/display/color_pipeline.py
src/sage_lib/visualization/display/colormaps.py
src/sage_lib/visualization/display/component_rules.py
src/sage_lib/visualization/display/compositor.py
src/sage_lib/visualization/display/controller.py
src/sage_lib/visualization/display/layer_factory.py
src/sage_lib/visualization/display/layer_set.py
src/sage_lib/visualization/display/layer_templates.py
src/sage_lib/visualization/display/layers.py
src/sage_lib/visualization/display/material_tbo.py
src/sage_lib/visualization/display/named_selections.py
src/sage_lib/visualization/display/presets.py
src/sage_lib/visualization/display/pretty_knobs.py
src/sage_lib/visualization/display/pretty_settings_io.py
src/sage_lib/visualization/display/protein_visibility.py
src/sage_lib/visualization/display/representation_registry.py
src/sage_lib/visualization/display/representation_set.py
src/sage_lib/visualization/display/representations.py
src/sage_lib/visualization/display/selector_language.py
src/sage_lib/visualization/display/selectors.py
src/sage_lib/visualization/display/semantic_biomolecules.py
src/sage_lib/visualization/display/semantic_generic.py
src/sage_lib/visualization/display/semantic_groups.py
src/sage_lib/visualization/display/semantic_materials.py
src/sage_lib/visualization/display/serialization.py
src/sage_lib/visualization/display/skin_sss.py
src/sage_lib/visualization/display/state.py
src/sage_lib/visualization/display/system_classification.py
src/sage_lib/visualization/display/validation.py
src/sage_lib/visualization/display/visual_state.py
src/sage_lib/visualization/io/__init__.py
src/sage_lib/visualization/io/exporters.py
src/sage_lib/visualization/io/fetch_cod.py
src/sage_lib/visualization/io/fetch_mp.py
src/sage_lib/visualization/io/fetch_optimade.py
src/sage_lib/visualization/io/fetch_pubchem.py
src/sage_lib/visualization/io/fetch_rcsb.py
src/sage_lib/visualization/io/mesh_export_gltf.py
src/sage_lib/visualization/io/mesh_export_stl.py
src/sage_lib/visualization/io/model_catalog.py
src/sage_lib/visualization/io/providers.py
src/sage_lib/visualization/io/structure_loader.py
src/sage_lib/visualization/live_lab/__init__.py
src/sage_lib/visualization/live_lab/api.py
src/sage_lib/visualization/live_lab/autocomplete.py
src/sage_lib/visualization/live_lab/console.py
src/sage_lib/visualization/live_lab/plot_bridge.py
src/sage_lib/visualization/live_lab/script_io.py
src/sage_lib/visualization/modules/__init__.py
src/sage_lib/visualization/modules/ezga_analysis.py
src/sage_lib/visualization/motif_studio/__init__.py
src/sage_lib/visualization/motif_studio/annotate.py
src/sage_lib/visualization/motif_studio/config.py
src/sage_lib/visualization/motif_studio/cycle_seeds.py
src/sage_lib/visualization/motif_studio/entropy.py
src/sage_lib/visualization/motif_studio/graph_layout.py
src/sage_lib/visualization/motif_studio/pipeline.py
src/sage_lib/visualization/motif_studio/progress.py
src/sage_lib/visualization/motif_studio/results.py
src/sage_lib/visualization/motif_studio/run_cache.py
src/sage_lib/visualization/motif_studio/schema.py
src/sage_lib/visualization/motif_studio/seed_sources.py
src/sage_lib/visualization/renderer/__init__.py
src/sage_lib/visualization/renderer/ao_core.py
src/sage_lib/visualization/renderer/blob.py
src/sage_lib/visualization/renderer/bond_renderer.py
src/sage_lib/visualization/renderer/dither3d.py
src/sage_lib/visualization/renderer/dither3d_core.py
src/sage_lib/visualization/renderer/export_writer.py
src/sage_lib/visualization/renderer/gl_caps.py
src/sage_lib/visualization/renderer/godray_core.py
src/sage_lib/visualization/renderer/id_buffer.py
src/sage_lib/visualization/renderer/line_renderer.py
src/sage_lib/visualization/renderer/matcap.py
src/sage_lib/visualization/renderer/matcap_core.py
src/sage_lib/visualization/renderer/mesh_export_geometry.py
src/sage_lib/visualization/renderer/mesh_io.py
src/sage_lib/visualization/renderer/mesh_props.py
src/sage_lib/visualization/renderer/mesh_props_energy.py
src/sage_lib/visualization/renderer/mesh_props_kit.py
src/sage_lib/visualization/renderer/mesh_props_lab.py
src/sage_lib/visualization/renderer/mesh_props_nano.py
src/sage_lib/visualization/renderer/mesh_props_nature.py
src/sage_lib/visualization/renderer/mesh_props_symbols.py
src/sage_lib/visualization/renderer/mesh_renderer.py
src/sage_lib/visualization/renderer/mesh_thumbnail.py
src/sage_lib/visualization/renderer/pcss_core.py
src/sage_lib/visualization/renderer/picking_renderer.py
src/sage_lib/visualization/renderer/polyhedron_renderer.py
src/sage_lib/visualization/renderer/post_process.py
src/sage_lib/visualization/renderer/protein_renderer.py
src/sage_lib/visualization/renderer/quad_renderer.py
src/sage_lib/visualization/renderer/sdf_renderer.py
src/sage_lib/visualization/renderer/shaders.py
src/sage_lib/visualization/renderer/sphere_renderer.py
src/sage_lib/visualization/renderer/ssgi_core.py
src/sage_lib/visualization/renderer/taa_core.py
src/sage_lib/visualization/renderer/texel_renderer.py
src/sage_lib/visualization/renderer/utils.py
src/sage_lib/visualization/renderer/volume_renderer.py
src/sage_lib/visualization/reporting/__init__.py
src/sage_lib/visualization/reporting/report_builder.py
src/sage_lib/visualization/reporting/report_html.py
src/sage_lib/visualization/reporting/report_pdf.py
src/sage_lib/visualization/session/__init__.py
src/sage_lib/visualization/session/action_journal.py
src/sage_lib/visualization/session/param_spec.py
src/sage_lib/visualization/session/replay.py
src/sage_lib/visualization/session/session_bundle.py
src/sage_lib/visualization/simulation/__init__.py
src/sage_lib/visualization/simulation/colliders.py
src/sage_lib/visualization/simulation/domain.py
src/sage_lib/visualization/simulation/emitters.py
src/sage_lib/visualization/simulation/particles.py
src/sage_lib/visualization/simulation/phases.py
src/sage_lib/visualization/simulation/render_bridge.py
src/sage_lib/visualization/simulation/scenarios.py
src/sage_lib/visualization/simulation/settings.py
src/sage_lib/visualization/simulation/solvers.py
src/sage_lib/visualization/simulation/surface.py
src/sage_lib/visualization/simulation/timeline.py
src/sage_lib/visualization/simulation/world.py
src/sage_lib/visualization/ui/__init__.py
src/sage_lib/visualization/ui/app_assistant.py
src/sage_lib/visualization/ui/build_inspector.py
src/sage_lib/visualization/ui/builder_panel.py
src/sage_lib/visualization/ui/display_analysis_hub.py
src/sage_lib/visualization/ui/display_layer_editor.py
src/sage_lib/visualization/ui/display_main_panel.py
src/sage_lib/visualization/ui/display_mutations.py
src/sage_lib/visualization/ui/display_named_selections.py
src/sage_lib/visualization/ui/display_output.py
src/sage_lib/visualization/ui/display_playback.py
src/sage_lib/visualization/ui/display_preset_browser.py
src/sage_lib/visualization/ui/display_representations.py
src/sage_lib/visualization/ui/display_scientific_geometry.py
src/sage_lib/visualization/ui/display_status_bar.py
src/sage_lib/visualization/ui/display_structure_overview.py
src/sage_lib/visualization/ui/display_workflow_history.py
src/sage_lib/visualization/ui/distributions_panel.py
src/sage_lib/visualization/ui/exit_dialog.py
src/sage_lib/visualization/ui/fetch_by_id_panel.py
src/sage_lib/visualization/ui/imgui_guard.py
src/sage_lib/visualization/ui/interactions_panel.py
src/sage_lib/visualization/ui/measurement_workbench.py
src/sage_lib/visualization/ui/model_library.py
src/sage_lib/visualization/ui/multi_file_overview.py
src/sage_lib/visualization/ui/normal_modes_panel.py
src/sage_lib/visualization/ui/notifications.py
src/sage_lib/visualization/ui/performance_panel.py
src/sage_lib/visualization/ui/pes_cv_workbench.py
src/sage_lib/visualization/ui/pes_explorer_panel.py
src/sage_lib/visualization/ui/plot_canvas.py
src/sage_lib/visualization/ui/plot_math.py
src/sage_lib/visualization/ui/plots.py
src/sage_lib/visualization/ui/preferences_io.py
src/sage_lib/visualization/ui/recent_files.py
src/sage_lib/visualization/ui/report_generator_panel.py
src/sage_lib/visualization/ui/selection_sets.py
src/sage_lib/visualization/ui/selections_panel.py
src/sage_lib/visualization/ui/session_io.py
src/sage_lib/visualization/ui/theme.py
src/sage_lib/visualization/ui/widgets.py
src/sage_lib/visualization/ui/workspace_layout.py
src/sage_lib/visualization/ui/workspace_status_bar.py
src/sage_lib/visualization/ui/z_profile_panel.py
src/sage_lib/visualization/ui/ensemble_analysis/__init__.py
src/sage_lib/visualization/ui/ensemble_analysis/batch_export.py
src/sage_lib/visualization/ui/ensemble_analysis/cache_manager_ui.py
src/sage_lib/visualization/ui/ensemble_analysis/job_ui.py
src/sage_lib/visualization/ui/ensemble_analysis/navigate.py
src/sage_lib/visualization/ui/ensemble_analysis/panel.py
src/sage_lib/visualization/ui/ensemble_analysis/plot_customize.py
src/sage_lib/visualization/ui/ensemble_analysis/plot_export.py
src/sage_lib/visualization/ui/ensemble_analysis/plot_widget.py
src/sage_lib/visualization/ui/ensemble_analysis/state.py
src/sage_lib/visualization/ui/ensemble_analysis/tab_distributions.py
src/sage_lib/visualization/ui/ensemble_analysis/tab_overview.py
src/sage_lib/visualization/ui/ensemble_analysis/tab_representatives.py
src/sage_lib/visualization/ui/ensemble_analysis/tab_scatter.py
src/sage_lib/visualization/ui/ensemble_analysis/tab_table.py
src/sage_lib/visualization/ui/ensemble_analysis/ui_kit.py
src/sage_lib/visualization/ui/model_studio/__init__.py
src/sage_lib/visualization/ui/model_studio/gallery.py
src/sage_lib/visualization/ui/model_studio/materials_tab.py
src/sage_lib/visualization/ui/model_studio/panel.py
src/sage_lib/visualization/ui/model_studio/scene_tab.py
src/sage_lib/visualization/ui/model_studio/shared.py
src/sage_lib/visualization/ui/model_studio/simulation_tab.py
src/sage_lib/visualization/ui/model_studio/thumbnails.py
src/sage_lib/visualization/ui/motif_studio/__init__.py
src/sage_lib/visualization/ui/motif_studio/common.py
src/sage_lib/visualization/ui/motif_studio/connectivity_view.py
src/sage_lib/visualization/ui/motif_studio/copies_result.py
src/sage_lib/visualization/ui/motif_studio/entropy_plots.py
src/sage_lib/visualization/ui/motif_studio/entropy_select.py
src/sage_lib/visualization/ui/motif_studio/fields.py
src/sage_lib/visualization/ui/motif_studio/graph_view.py
src/sage_lib/visualization/ui/motif_studio/panel.py
src/sage_lib/visualization/ui/motif_studio/plots.py
src/sage_lib/visualization/ui/motif_studio/state.py
src/sage_lib/visualization/ui/motif_studio/tab_copies.py
src/sage_lib/visualization/ui/motif_studio/tab_entropy.py
src/sage_lib/visualization/ui/motif_studio/tab_families.py
src/sage_lib/visualization/ui/motif_studio/tab_grammar.py
src/sage_lib/visualization/ui/motif_studio/tab_graphs.py
src/sage_lib/visualization/ui/motif_studio/tab_hierarchy.py
src/sage_lib/visualization/ui/motif_studio/tab_model.py
src/sage_lib/visualization/ui/motif_studio/tab_run.py
src/sage_lib/visualization/ui/motif_studio/tab_setup.py
src/sage_lib/visualization/ui/motif_studio/tab_structure.py
src/sage_lib/visualization/ui/motif_studio/tab_thermo.py
src/sage_lib/visualization/ui/motif_studio/tab_vocabulary.py
src/sage_lib/visualization/ui/motif_studio/visuals.py
src/sage_lib/visualization/ui/workflow_studio/__init__.py
src/sage_lib/visualization/ui/workflow_studio/agent_conversation.py
src/sage_lib/visualization/ui/workflow_studio/agent_testing.py
src/sage_lib/visualization/ui/workflow_studio/canvas_navigation.py
src/sage_lib/visualization/ui/workflow_studio/cleanup_controls.py
src/sage_lib/visualization/ui/workflow_studio/common.py
src/sage_lib/visualization/ui/workflow_studio/figure_options.py
src/sage_lib/visualization/ui/workflow_studio/file_previews.py
src/sage_lib/visualization/ui/workflow_studio/form_engine.py
src/sage_lib/visualization/ui/workflow_studio/inline_plot.py
src/sage_lib/visualization/ui/workflow_studio/json_editor.py
src/sage_lib/visualization/ui/workflow_studio/node_results.py
src/sage_lib/visualization/ui/workflow_studio/panel.py
src/sage_lib/visualization/ui/workflow_studio/project_controls.py
src/sage_lib/visualization/ui/workflow_studio/render_options.py
src/sage_lib/visualization/ui/workflow_studio/run_controls.py
src/sage_lib/visualization/ui/workflow_studio/sampling_assistant.py
src/sage_lib/visualization/ui/workflow_studio/sampling_controls.py
src/sage_lib/visualization/ui/workflow_studio/sampling_expert.py
src/sage_lib/visualization/ui/workflow_studio/structure_preview.py
src/sage_lib/visualization/ui/workflow_studio/tab_agent.py
src/sage_lib/visualization/ui/workflow_studio/tab_analysis.py
src/sage_lib/visualization/ui/workflow_studio/tab_bio.py
src/sage_lib/visualization/ui/workflow_studio/tab_dataset_ops.py
src/sage_lib/visualization/ui/workflow_studio/tab_diagnostics.py
src/sage_lib/visualization/ui/workflow_studio/tab_download.py
src/sage_lib/visualization/ui/workflow_studio/tab_examples.py
src/sage_lib/visualization/ui/workflow_studio/tab_export.py
src/sage_lib/visualization/ui/workflow_studio/tab_export_node.py
src/sage_lib/visualization/ui/workflow_studio/tab_extra_nodes.py
src/sage_lib/visualization/ui/workflow_studio/tab_extract.py
src/sage_lib/visualization/ui/workflow_studio/tab_files.py
src/sage_lib/visualization/ui/workflow_studio/tab_filtering.py
src/sage_lib/visualization/ui/workflow_studio/tab_generate.py
src/sage_lib/visualization/ui/workflow_studio/tab_pipeline.py
src/sage_lib/visualization/ui/workflow_studio/tab_plots.py
src/sage_lib/visualization/ui/workflow_studio/tab_postprocessing.py
src/sage_lib/visualization/ui/workflow_studio/tab_python.py
src/sage_lib/visualization/ui/workflow_studio/tab_results.py
src/sage_lib/visualization/ui/workflow_studio/tab_sampling.py
src/sage_lib/visualization/ui/workflow_studio/tab_setup.py
src/sage_lib/visualization/ui/workflow_studio/tab_structure_edit.py
src/sage_lib/visualization/ui/workflow_studio/tab_surface.py
src/sage_lib/visualization/ui/workflow_studio/thermodynamic_controls.py
src/sage_lib/visualization/viz_mixins/__init__.py
src/sage_lib/visualization/viz_mixins/bio.py
src/sage_lib/visualization/viz_mixins/camera.py
src/sage_lib/visualization/viz_mixins/file_overlays.py
src/sage_lib/visualization/viz_mixins/materials.py
src/sage_lib/visualization/viz_mixins/normal_modes.py
src/sage_lib/visualization/viz_mixins/render.py
src/sage_lib/visualization/viz_mixins/scene.py
src/sage_lib/visualization/viz_mixins/selection_tools.py
src/sage_lib/visualization/viz_mixins/simulation.py
src/sage_lib/visualization/viz_mixins/ui.py
src/sage_lib/visualization/webgui/__init__.py
src/sage_lib/visualization/webgui/glproxy.py
src/sage_lib/visualization/webgui/session.py
src/sage_lib/visualization/webgui/transport.py
src/sage_lib/visualization/webgui/static/app.js
src/sage_lib/visualization/webgui/static/glreplay.js
src/sage_lib/visualization/webgui/static/index.html
src/sage_lib/visualization/webviz/__init__.py
src/sage_lib/visualization/webviz/payload.py
src/sage_lib/visualization/webviz/presets.py
src/sage_lib/visualization/webviz/server.py
src/sage_lib/visualization/webviz/domains/__init__.py
src/sage_lib/visualization/webviz/domains/analysis_panels.py
src/sage_lib/visualization/webviz/domains/bio_cartoon_compute.py
src/sage_lib/visualization/webviz/domains/builder_workshop.py
src/sage_lib/visualization/webviz/domains/camera_navigation_endpoints.py
src/sage_lib/visualization/webviz/domains/color_modes.py
src/sage_lib/visualization/webviz/domains/ensemble_filter_export.py
src/sage_lib/visualization/webviz/domains/ezga_analysis.py
src/sage_lib/visualization/webviz/domains/glass_subsurface_shading.py
src/sage_lib/visualization/webviz/domains/lighting_pretty.py
src/sage_lib/visualization/webviz/domains/representations_materials.py
src/sage_lib/visualization/webviz/domains/selection_measurement_query.py
src/sage_lib/visualization/webviz/domains/session_playback.py
src/sage_lib/visualization/webviz/domains/volumetric_isosurface.py
src/sage_lib/visualization/webviz/static/index.html
src/sage_lib/visualization/workflow_studio/__init__.py
src/sage_lib/visualization/workflow_studio/agent_activity.py
src/sage_lib/visualization/workflow_studio/agent_biomolecules.py
src/sage_lib/visualization/workflow_studio/agent_client.py
src/sage_lib/visualization/workflow_studio/agent_context.py
src/sage_lib/visualization/workflow_studio/agent_credentials.py
src/sage_lib/visualization/workflow_studio/agent_handoff.py
src/sage_lib/visualization/workflow_studio/agent_local.py
src/sage_lib/visualization/workflow_studio/agent_mcp.py
src/sage_lib/visualization/workflow_studio/agent_memory.py
src/sage_lib/visualization/workflow_studio/agent_operator_validation.py
src/sage_lib/visualization/workflow_studio/agent_testing.py
src/sage_lib/visualization/workflow_studio/agent_tools.py
src/sage_lib/visualization/workflow_studio/agent_usage.py
src/sage_lib/visualization/workflow_studio/analysis_core.py
src/sage_lib/visualization/workflow_studio/artifacts.py
src/sage_lib/visualization/workflow_studio/canvas_layout.py
src/sage_lib/visualization/workflow_studio/cleanup.py
src/sage_lib/visualization/workflow_studio/codegen.py
src/sage_lib/visualization/workflow_studio/console_checkpoint.py
src/sage_lib/visualization/workflow_studio/dataset_ops.py
src/sage_lib/visualization/workflow_studio/diagnostics.py
src/sage_lib/visualization/workflow_studio/docking_core.py
src/sage_lib/visualization/workflow_studio/download_core.py
src/sage_lib/visualization/workflow_studio/engine_progress.py
src/sage_lib/visualization/workflow_studio/example_pipelines.py
src/sage_lib/visualization/workflow_studio/execution.py
src/sage_lib/visualization/workflow_studio/export_core.py
src/sage_lib/visualization/workflow_studio/extra_nodes.py
src/sage_lib/visualization/workflow_studio/ezga_bridge.py
src/sage_lib/visualization/workflow_studio/ezga_compile.py
src/sage_lib/visualization/workflow_studio/ezga_options.py
src/sage_lib/visualization/workflow_studio/field_meta.py
src/sage_lib/visualization/workflow_studio/file_library.py
src/sage_lib/visualization/workflow_studio/form_schema.py
src/sage_lib/visualization/workflow_studio/generation_presets.py
src/sage_lib/visualization/workflow_studio/history.py
src/sage_lib/visualization/workflow_studio/interface_analysis.py
src/sage_lib/visualization/workflow_studio/loaded_data.py
src/sage_lib/visualization/workflow_studio/node_catalog.py
src/sage_lib/visualization/workflow_studio/node_io.py
src/sage_lib/visualization/workflow_studio/operator_options.py
src/sage_lib/visualization/workflow_studio/partition_io.py
src/sage_lib/visualization/workflow_studio/plot_presets.py
src/sage_lib/visualization/workflow_studio/plot_view.py
src/sage_lib/visualization/workflow_studio/postprocessing_core.py
src/sage_lib/visualization/workflow_studio/preview_worker.py
src/sage_lib/visualization/workflow_studio/project_archive.py
src/sage_lib/visualization/workflow_studio/property_series.py
src/sage_lib/visualization/workflow_studio/python_node.py
src/sage_lib/visualization/workflow_studio/run_logging.py
src/sage_lib/visualization/workflow_studio/sage_render.py
src/sage_lib/visualization/workflow_studio/sampling_defaults.py
src/sage_lib/visualization/workflow_studio/sampling_guides.py
src/sage_lib/visualization/workflow_studio/sampling_modes.py
src/sage_lib/visualization/workflow_studio/sampling_presets.py
src/sage_lib/visualization/workflow_studio/sampling_protocols.py
src/sage_lib/visualization/workflow_studio/sampling_run.py
src/sage_lib/visualization/workflow_studio/settings_io.py
src/sage_lib/visualization/workflow_studio/slurm.py
src/sage_lib/visualization/workflow_studio/stage_graph.py
src/sage_lib/visualization/workflow_studio/standalone.py
src/sage_lib/visualization/workflow_studio/step_specs.py
src/sage_lib/visualization/workflow_studio/structure_edit_ops.py
src/sage_lib/visualization/workflow_studio/structure_generation.py
src/sage_lib/visualization/workflow_studio/structure_plot.py
src/sage_lib/visualization/workflow_studio/structure_views.py
src/sage_lib/visualization/workflow_studio/surface_examples.py
src/sage_lib/visualization/workflow_studio/surface_workflows.py
src/sage_lib/visualization/workflow_studio/tested_input_export.py
src/sage_lib/visualization/workflow_studio/thermodynamic_protocols.py
src/sage_lib/visualization/workflow_studio/validation_bridge.py
src/sage_lib/visualization/workflow_studio/workspace.py
test/test_agent_setup.py
test/test_align_ensemble_chaindisp.py
test/test_analysis_cores.py
test/test_app_assistant.py
test/test_assistant_api_keys.py
test/test_assistant_composition.py
test/test_assistant_context_compaction.py
test/test_assistant_ensemble.py
test/test_assistant_filter.py
test/test_assistant_llm_efficiency.py
test/test_assistant_motifs.py
test/test_assistant_query.py
test/test_assistant_ui_logic.py
test/test_assistant_workspace.py
test/test_bio_classification.py
test/test_bond_connectivity_cache.py
test/test_cartoon_coloring.py
test/test_claude_setup.py
test/test_comparison_core.py
test/test_displacement_field.py
test/test_distributions.py
test/test_generate_gui_remote_dispatch.py
test/test_jobs_manager.py
test/test_magic_finder_nav.py
test/test_material_tbo_cache.py
test/test_mcp_gui_bridge.py
test/test_mcp_server.py
test/test_motif_entropy.py
test/test_motif_studio.py
test/test_normal_modes.py
test/test_overlay_bond_hidden.py
test/test_oxide_surfaces.py
test/test_pretty_knobs.py
test/test_pretty_settings_io.py
test/test_protein_ribbon_geometry.py
test/test_remote_launcher.py
test/test_remote_partition_provider.py
test/test_remote_partition_storage.py
test/test_replica_cull.py
test/test_ribbon_async_build.py
test/test_setup_agent_unified.py
test/test_super_overlay_cache.py
test/test_uniform_location_cache.py
test/test_vector_property_arrows.py
test/test_workflow_studio_agent_activity.py
test/test_workflow_studio_agent_autorepair.py
test/test_workflow_studio_agent_biomolecules.py
test/test_workflow_studio_agent_context.py
test/test_workflow_studio_agent_handoff.py
test/test_workflow_studio_agent_memory.py
test/test_workflow_studio_agent_streaming.py
test/test_workflow_studio_agent_testing.py
test/test_workflow_studio_analysis_core.py
test/test_workflow_studio_branches.py
test/test_workflow_studio_canvas_layout.py
test/test_workflow_studio_checkpoints.py
test/test_workflow_studio_codegen.py
test/test_workflow_studio_compile.py
test/test_workflow_studio_dataset_ops.py
test/test_workflow_studio_download_core.py
test/test_workflow_studio_example_pipelines.py
test/test_workflow_studio_execution.py
test/test_workflow_studio_export_controls.py
test/test_workflow_studio_ezga_bridge.py
test/test_workflow_studio_file_library.py
test/test_workflow_studio_form_schema.py
test/test_workflow_studio_guided_workbench.py
test/test_workflow_studio_history.py
test/test_workflow_studio_live_outputs.py
test/test_workflow_studio_loaded_input.py
test/test_workflow_studio_molecular_workbench.py
test/test_workflow_studio_native_protocols.py
test/test_workflow_studio_node_catalog.py
test/test_workflow_studio_partition_io.py
test/test_workflow_studio_postprocessing_core.py
test/test_workflow_studio_preview_recovery.py
test/test_workflow_studio_project_archive.py
test/test_workflow_studio_property_series.py
test/test_workflow_studio_python_agents.py
test/test_workflow_studio_run_stage.py
test/test_workflow_studio_sampling_modes.py
test/test_workflow_studio_sampling_usability.py
test/test_workflow_studio_settings_io.py
test/test_workflow_studio_slurm.py
test/test_workflow_studio_standalone.py
test/test_workflow_studio_step_specs.py
test/test_workflow_studio_structure_edit_ops.py
test/test_workflow_studio_structure_generation.py
test/test_workflow_studio_surface_workflows.py
test/test_workflow_studio_tab_filtering.py
test/test_workflow_studio_validation_bridge.py
test/test_workflow_studio_workspace.py