MANIFEST.in
README.md
pyproject.toml
requirements.txt
scilink/__init__.py
scilink/auth.py
scilink/executors.py
scilink/mcp_client.py
scilink/mcp_server.py
scilink/tracing.py
scilink.egg-info/PKG-INFO
scilink.egg-info/SOURCES.txt
scilink.egg-info/dependency_links.txt
scilink.egg-info/entry_points.txt
scilink.egg-info/requires.txt
scilink.egg-info/top_level.txt
scilink/agents/__init__.py
scilink/agents/exp_agents/__init__.py
scilink/agents/exp_agents/_deprecation.py
scilink/agents/exp_agents/analysis_orchestrator.py
scilink/agents/exp_agents/analysis_orchestrator_tools.py
scilink/agents/exp_agents/base_agent.py
scilink/agents/exp_agents/curve_fitting_agent.py
scilink/agents/exp_agents/feature_table.py
scilink/agents/exp_agents/human_feedback.py
scilink/agents/exp_agents/hyperspectral_analysis_agent.py
scilink/agents/exp_agents/image_analysis_agent.py
scilink/agents/exp_agents/instruct.py
scilink/agents/exp_agents/metadata_converter.py
scilink/agents/exp_agents/preprocess.py
scilink/agents/exp_agents/quality_gate.py
scilink/agents/exp_agents/recommendation_agent.py
scilink/agents/exp_agents/utils.py
scilink/agents/exp_agents/controllers/base_controllers.py
scilink/agents/exp_agents/controllers/curve_fitting_controllers.py
scilink/agents/exp_agents/controllers/hyperspectral_controllers.py
scilink/agents/exp_agents/controllers/image_analysis_controllers.py
scilink/agents/exp_agents/pipelines/curve_fitting_pipelines.py
scilink/agents/exp_agents/pipelines/hyperspectral_pipelines.py
scilink/agents/exp_agents/pipelines/image_analysis_pipelines.py
scilink/agents/lit_agents/__init__.py
scilink/agents/lit_agents/_deprecation.py
scilink/agents/lit_agents/instruct.py
scilink/agents/lit_agents/literature_agent.py
scilink/agents/lit_agents/molecules_agent.py
scilink/agents/lit_agents/novelty_scorer.py
scilink/agents/lit_agents/optimize_query.py
scilink/agents/lit_agents/optimize_query_for_analysis.py
scilink/agents/meta_agent/__init__.py
scilink/agents/meta_agent/meta_orchestrator.py
scilink/agents/meta_agent/meta_orchestrator_tools.py
scilink/agents/meta_agent/telemetry.py
scilink/agents/planning_agents/__init__.py
scilink/agents/planning_agents/_deprecation.py
scilink/agents/planning_agents/base_agent.py
scilink/agents/planning_agents/bo_agent.py
scilink/agents/planning_agents/bo_tools.py
scilink/agents/planning_agents/html_generator.py
scilink/agents/planning_agents/instruct.py
scilink/agents/planning_agents/orchestrator_tools.py
scilink/agents/planning_agents/parser_utils.py
scilink/agents/planning_agents/planning_agent.py
scilink/agents/planning_agents/planning_orchestrator.py
scilink/agents/planning_agents/planning_rag.py
scilink/agents/planning_agents/repo_loader.py
scilink/agents/planning_agents/scalarizer_agent.py
scilink/agents/planning_agents/user_interface.py
scilink/agents/sim_agents/__init__.py
scilink/agents/sim_agents/_ase_runner.py
scilink/agents/sim_agents/_deprecation.py
scilink/agents/sim_agents/_potential.py
scilink/agents/sim_agents/atomate2_utils.py
scilink/agents/sim_agents/base_agent.py
scilink/agents/sim_agents/dft_orchestrator.py
scilink/agents/sim_agents/force_field_agent.py
scilink/agents/sim_agents/instruct.py
scilink/agents/sim_agents/lammps_agent.py
scilink/agents/sim_agents/lammps_analysis.py
scilink/agents/sim_agents/lammps_analysis_updater.py
scilink/agents/sim_agents/lammps_orchestrator.py
scilink/agents/sim_agents/lammps_updater.py
scilink/agents/sim_agents/lammps_utils.py
scilink/agents/sim_agents/md_simulation_agent.py
scilink/agents/sim_agents/mlip_agent.py
scilink/agents/sim_agents/packmol_agent.py
scilink/agents/sim_agents/periodic_dft_agent.py
scilink/agents/sim_agents/post_run_analysis.py
scilink/agents/sim_agents/simulation_orchestrator.py
scilink/agents/sim_agents/simulation_orchestrator_tools.py
scilink/agents/sim_agents/simulation_router.py
scilink/agents/sim_agents/skill_graduation.py
scilink/agents/sim_agents/structure_agent.py
scilink/agents/sim_agents/structure_orchestrator.py
scilink/agents/sim_agents/structure_planner.py
scilink/agents/sim_agents/tools.py
scilink/agents/sim_agents/utils.py
scilink/agents/sim_agents/val_agent.py
scilink/agents/sim_agents/vasp_agent.py
scilink/agents/sim_agents/vasp_config.py
scilink/agents/sim_agents/vasp_quality.py
scilink/agents/sim_agents/vasp_updater.py
scilink/agents/skills/__init__.py
scilink/cli/__init__.py
scilink/cli/analyze.py
scilink/cli/main.py
scilink/cli/meta.py
scilink/cli/plan.py
scilink/cli/prepare_ff.py
scilink/cli/serve.py
scilink/cli/simulate.py
scilink/cli/ui.py
scilink/hpc/__init__.py
scilink/hpc/connection.py
scilink/hpc/probe.py
scilink/hpc/scheduler.py
scilink/knowledge/__init__.py
scilink/knowledge/_deprecation.py
scilink/knowledge/knowledge_base.py
scilink/knowledge/rag_engine.py
scilink/knowledge/synthesis.py
scilink/parsers/__init__.py
scilink/parsers/excel_parser.py
scilink/parsers/extract.py
scilink/parsers/ingestor.py
scilink/parsers/ocr.py
scilink/parsers/pdf_parser.py
scilink/skills/__init__.py
scilink/skills/loader.py
scilink/skills/_shared/__init__.py
scilink/skills/_shared/_registry.py
scilink/skills/_shared/_spec.py
scilink/skills/_shared/atomistic_model_manager.py
scilink/skills/_shared/curve_fitting_tools.py
scilink/skills/_shared/fft_nmf.py
scilink/skills/_shared/image_analysis_tools.py
scilink/skills/_shared/image_processor.py
scilink/skills/_shared/mlip_tools.py
scilink/skills/_shared/particle_analyzer.py
scilink/skills/_shared/sam.py
scilink/skills/curve_fitting/__init__.py
scilink/skills/curve_fitting/xps/__init__.py
scilink/skills/curve_fitting/xps/xps.md
scilink/skills/curve_fitting/xrd_profile/__init__.py
scilink/skills/curve_fitting/xrd_profile/background.py
scilink/skills/curve_fitting/xrd_profile/fit_profile.py
scilink/skills/curve_fitting/xrd_profile/scherrer.py
scilink/skills/curve_fitting/xrd_profile/williamson_hall.py
scilink/skills/curve_fitting/xrd_profile/xrd_profile.md
scilink/skills/force_field/__init__.py
scilink/skills/force_field/amber/__init__.py
scilink/skills/force_field/amber/amber.md
scilink/skills/force_field/amber/amber.py
scilink/skills/hyperspectral/__init__.py
scilink/skills/hyperspectral/eels/__init__.py
scilink/skills/hyperspectral/eels/eels.md
scilink/skills/hyperspectral/eels/eels.py
scilink/skills/hyperspectral/eels/spectral_unmixer.py
scilink/skills/image_analysis/__init__.py
scilink/skills/image_analysis/afm/__init__.py
scilink/skills/image_analysis/afm/afm.md
scilink/skills/image_analysis/atomic_stem/__init__.py
scilink/skills/image_analysis/atomic_stem/atom_finding.py
scilink/skills/image_analysis/atomic_stem/atomic_stem.md
scilink/skills/image_analysis/atomic_stem/atomic_stem.py
scilink/skills/image_analysis/overlapping_objects/__init__.py
scilink/skills/image_analysis/overlapping_objects/overlapping_objects.md
scilink/skills/image_analysis/stm_cafm/__init__.py
scilink/skills/image_analysis/stm_cafm/stm_cafm.md
scilink/skills/machine_learning_potentials/__init__.py
scilink/skills/machine_learning_potentials/chgnet/__init__.py
scilink/skills/machine_learning_potentials/chgnet/chgnet.md
scilink/skills/machine_learning_potentials/general/__init__.py
scilink/skills/machine_learning_potentials/general/general.md
scilink/skills/machine_learning_potentials/mace/__init__.py
scilink/skills/machine_learning_potentials/mace/mace.md
scilink/skills/molecular_dynamics/__init__.py
scilink/skills/molecular_dynamics/lammps/__init__.py
scilink/skills/molecular_dynamics/lammps/lammps.md
scilink/skills/molecular_dynamics/lammps/lammps.py
scilink/skills/periodic_dft/__init__.py
scilink/skills/periodic_dft/qe/__init__.py
scilink/skills/periodic_dft/qe/qe.md
scilink/skills/periodic_dft/vasp/__init__.py
scilink/skills/periodic_dft/vasp/vasp.md
scilink/skills/planning/__init__.py
scilink/skills/structure_generation/__init__.py
scilink/skills/structure_generation/aimsgb/__init__.py
scilink/skills/structure_generation/aimsgb/aimsgb.md
scilink/skills/structure_generation/biomolecular/__init__.py
scilink/skills/structure_generation/biomolecular/biomolecular.md
scilink/skills/structure_generation/condensed/__init__.py
scilink/skills/structure_generation/condensed/condensed.md
scilink/skills/structure_generation/crystal/__init__.py
scilink/skills/structure_generation/crystal/crystal.md
scilink/skills/structure_generation/molecular/__init__.py
scilink/skills/structure_generation/molecular/molecular.md
scilink/skills/structure_matching/__init__.py
scilink/skills/structure_matching/_backends/__init__.py
scilink/skills/structure_matching/_backends/_base.py
scilink/skills/structure_matching/_backends/_cif_index.py
scilink/skills/structure_matching/_backends/cod.py
scilink/skills/structure_matching/_backends/local_cif.py
scilink/skills/structure_matching/_backends/materials_project.py
scilink/skills/structure_matching/xrd/__init__.py
scilink/skills/structure_matching/xrd/extract_peaks.py
scilink/skills/structure_matching/xrd/score_match_fast.py
scilink/skills/structure_matching/xrd/score_match_robust.py
scilink/skills/structure_matching/xrd/search_structures.py
scilink/skills/structure_matching/xrd/simulate_xrd.py
scilink/skills/structure_matching/xrd/wavelength.py
scilink/skills/structure_matching/xrd/xrd.md
scilink/ui/__init__.py
scilink/ui/_features.py
scilink/ui/app.py
scilink/ui/config.py
scilink/ui/output_capture.py
scilink/ui/state.py
scilink/ui/theme.py
scilink/ui/.streamlit/config.toml
scilink/ui/assets/avatar_agent.svg
scilink/ui/assets/avatar_user.svg
scilink/ui/assets/scilink_logo_v3_dark.svg
scilink/ui/assets/scilink_logo_v3_light.svg
scilink/ui/components/__init__.py
scilink/ui/components/chat_uploads.py
scilink/ui/components/engines.py
scilink/ui/components/file_viewer.py
scilink/ui/components/sidebar.py
scilink/ui/components/sim_workflow.py
scilink/ui/components/simulations.py
scilink/ui/components/skills.py
scilink/ui/components/telemetry.py
scilink/ui/components/tools_agents.py
scilink/ui/components/vasp_workflow.py
scilink/ui/components/wizard_state.py
scilink/utils/__init__.py
scilink/utils/available_software.py
scilink/utils/curve_preview.py
scilink/utils/hdf5_utils.py
scilink/wrappers/__init__.py
scilink/wrappers/litellm_wrapper.py
scilink/wrappers/llama_wrapper.py
scilink/wrappers/openai_wrapper.py
scilink/wrappers/openai_wrapper_embeddings.py
scilink/wrappers/openai_wrapper_tools.py
tests/test_172_image_reuse_live.py
tests/test_172_locked_reuse_live.py
tests/test_173_prior_paths_live.py
tests/test_adaptive_annealing.py
tests/test_adaptive_timeout_live.py
tests/test_backend_registration.py
tests/test_bo_advantage.py
tests/test_bo_convergence.py
tests/test_cif_index.py
tests/test_claim_count_live.py
tests/test_curve_fitting_stdout_parser.py
tests/test_extract_peaks.py
tests/test_knowledge_query.py
tests/test_lit_planner_injection.py
tests/test_lit_query_optimizer.py
tests/test_md_agent_smoke.py
tests/test_meta_buildupon_live.py
tests/test_meta_continuity_live.py
tests/test_meta_delegation_live.py
tests/test_mlip_agent_smoke.py
tests/test_mp_resolver.py
tests/test_orchestrator_parallel_chat_live.py
tests/test_orchestrator_per_call_workers_live.py
tests/test_orchestrator_routing_tool.py
tests/test_parallel_fanout_focused_live.py
tests/test_parallel_fanout_live.py
tests/test_parallel_fanout_multiregime_live.py
tests/test_parallel_speedup_live.py
tests/test_planning_campaigns.py
tests/test_preprocessing_orchestrator.py
tests/test_quality_gate.py
tests/test_quality_gate_verifier_integration.py
tests/test_safe_r2_helper.py
tests/test_scalarizer_sandbox.py
tests/test_score_match_robust.py
tests/test_simulation_orchestrator.py
tests/test_simulation_router.py
tests/test_skill_graduation.py
tests/test_skill_live.py
tests/test_skill_loader.py
tests/test_structure_backends.py
tests/test_structure_matching_smoke_live.py
tests/test_structure_matching_tools.py
tests/test_trend_multivar_live.py
tests/test_vasp_quality.py
tests/test_vasp_updater_fixes.py
tests/test_xrd_extensions_live.py
tests/test_xrd_extensions_realistic_live.py