MANIFEST.in
README.md
pyproject.toml
requirements.txt
analysis_session_20260331_105905/results/analysis_YBCO_tem_ImageAnalysis_20260331_110209_001/tier1/scripts/analysis_script.py
analysis_session_20260331_151653/results/analysis_YBCO_tem_ImageAnalysis_20260331_152204_001/tier1/scripts/analysis_script.py
analysis_session_20260331_155336/results/analysis_YBCO_tem_ImageAnalysis_20260331_155505_001/tier1/scripts/analysis_script.py
analysis_session_20260331_173929/results/analysis_nanoparticles_ImageAnalysis_20260331_174128_001/scripts/analysis_script.py
analysis_session_20260331_173929/results/analysis_nanoparticles_ImageAnalysis_20260331_174128_001/tier1/scripts/analysis_script.py
analysis_session_20260331_181850/results/analysis_polycrystalline_grains_ImageAnalysis_20260331_182206_001/tier1/scripts/analysis_script.py
analysis_session_20260331_184040/results/analysis_polycrystalline_grains_ImageAnalysis_20260331_184235_001/scripts/analysis_script.py
analysis_session_20260331_184040/results/analysis_polycrystalline_grains_ImageAnalysis_20260331_184235_001/tier1/scripts/analysis_script.py
analysis_session_20260331_212834/results/analysis__easy__AuNP_ImageAnalysis_20260331_212930_001/scripts/analysis_script.py
analysis_session_20260331_222758/results/analysis__medium__AuNP_binary_self-asse_ImageAnalysis_20260331_222948_001/scripts/analysis_script.py
analysis_session_20260331_222758/results/analysis__medium__AuNP_binary_self-asse_ImageAnalysis_20260331_222948_001/tier1/scripts/analysis_script.py
analysis_session_20260401_082752/results/analysis__easy__LLTO_ImageAnalysis_20260401_083025_001/tier1/scripts/analysis_script.py
analysis_session_20260401_114849/results/analysis__easy__Au_ImageAnalysis_20260401_115412_001/scripts/analysis_script.py
analysis_session_20260401_120813/results/analysis__easy__vaterite_ImageAnalysis_20260401_121021_001/tier1/scripts/analysis_script.py
analysis_session_20260401_122257/results/analysis__easy__vaterite_ImageAnalysis_20260401_122418_001/scripts/analysis_script.py
analysis_session_20260401_122257/results/analysis__easy__vaterite_ImageAnalysis_20260401_122418_001/tier1/scripts/analysis_script.py
docs/generate_annealing_figure.py
docs/generate_flowchart.py
docs/generate_learning_loop_figure.py
docs/generate_learning_loop_pptx.py
docs/md_to_docx.py
examples/continuous_learning_demo.py
examples/custom_image_tools.py
examples/custom_outlier_agent.py
examples/custom_peak_agent.py
examples/custom_stats_tools.py
examples/data/generate_raman_calibration.py
examples/data/generate_xps_ti2p.py
examples/data/test_batch_spectra/generate_test_data.py
examples/data/test_batch_spectra/simulate_spectra.py
examples/data/test_batch_spectra/simulate_spectra_v2.py
examples/data/test_batch_spectra/simulate_spectra_v3.py
examples/data/test_batch_tabular/generate_test_data.py
ftir_data/bruker_metadata_mapper.py
scilink/__init__.py
scilink/auth.py
scilink/executors.py
scilink/knowledge.py
scilink/mcp_client.py
scilink/mcp_server.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/__pycache__/__init__.cpython-312.pyc
scilink/__pycache__/__init__.cpython-313.pyc
scilink/__pycache__/auth.cpython-312.pyc
scilink/__pycache__/auth.cpython-313.pyc
scilink/__pycache__/executors.cpython-312.pyc
scilink/__pycache__/knowledge.cpython-312.pyc
scilink/__pycache__/mcp_client.cpython-312.pyc
scilink/__pycache__/mcp_server.cpython-312.pyc
scilink/agents/__init__.py
scilink/agents/__pycache__/__init__.cpython-312.pyc
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/atomistic_microscopy_agent.py
scilink/agents/exp_agents/base_agent.py
scilink/agents/exp_agents/curve_fitting_agent.py
scilink/agents/exp_agents/fft_microscopy_agent.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/orchestrator_agent.py
scilink/agents/exp_agents/preprocess.py
scilink/agents/exp_agents/recommendation_agent.py
scilink/agents/exp_agents/sam_microscopy_agent.py
scilink/agents/exp_agents/utils.py
scilink/agents/exp_agents/__pycache__/__init__.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/_deprecation.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/analysis_orchestrator.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/analysis_orchestrator_tools.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/atomistic_microscopy_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/base_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/curve_fitting_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/fft_microscopy_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/human_feedback.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/hyperspectral_analysis_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/image_analysis_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/instruct.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/metadata_converter.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/orchestrator_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/preprocess.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/recommendation_agent.cpython-312.pyc
scilink/agents/exp_agents/__pycache__/sam_microscopy_agent.cpython-312.pyc
scilink/agents/exp_agents/controllers/atomistic_microscopy_controllers.py
scilink/agents/exp_agents/controllers/base_controllers.py
scilink/agents/exp_agents/controllers/curve_fitting_controllers.py
scilink/agents/exp_agents/controllers/fft_microscopy_controllers.py
scilink/agents/exp_agents/controllers/hyperspectral_controllers.py
scilink/agents/exp_agents/controllers/image_analysis_controllers.py
scilink/agents/exp_agents/controllers/sam_microscopy_controllers.py
scilink/agents/exp_agents/controllers/__pycache__/atomistic_microscopy_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/base_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/curve_fitting_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/fft_microscopy_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/hyperspectral_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/image_analysis_controllers.cpython-312.pyc
scilink/agents/exp_agents/controllers/__pycache__/sam_microscopy_controllers.cpython-312.pyc
scilink/agents/exp_agents/pipelines/atomistic_microcopy_pipelines.py
scilink/agents/exp_agents/pipelines/curve_fitting_pipelines.py
scilink/agents/exp_agents/pipelines/fft_microscopy_pipelines.py
scilink/agents/exp_agents/pipelines/hyperspectral_pipelines.py
scilink/agents/exp_agents/pipelines/image_analysis_pipelines.py
scilink/agents/exp_agents/pipelines/sam_microscopy_pipelines.py
scilink/agents/exp_agents/pipelines/__pycache__/atomistic_microcopy_pipelines.cpython-312.pyc
scilink/agents/exp_agents/pipelines/__pycache__/curve_fitting_pipelines.cpython-312.pyc
scilink/agents/exp_agents/pipelines/__pycache__/fft_microscopy_pipelines.cpython-312.pyc
scilink/agents/exp_agents/pipelines/__pycache__/hyperspectral_pipelines.cpython-312.pyc
scilink/agents/exp_agents/pipelines/__pycache__/image_analysis_pipelines.cpython-312.pyc
scilink/agents/exp_agents/pipelines/__pycache__/sam_microscopy_pipelines.cpython-312.pyc
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/__pycache__/__init__.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/_deprecation.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/instruct.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/literature_agent.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/molecules_agent.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/novelty_scorer.cpython-312.pyc
scilink/agents/lit_agents/__pycache__/optimize_query.cpython-312.pyc
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/digest.txt
scilink/agents/planning_agents/excel_parser.py
scilink/agents/planning_agents/html_generator.py
scilink/agents/planning_agents/ingestor.py
scilink/agents/planning_agents/instruct.py
scilink/agents/planning_agents/knowledge_base.py
scilink/agents/planning_agents/orchestrator_tools.py
scilink/agents/planning_agents/parser_utils.py
scilink/agents/planning_agents/pdf_parser.py
scilink/agents/planning_agents/planning_agent.py
scilink/agents/planning_agents/planning_orchestrator.py
scilink/agents/planning_agents/rag_engine.py
scilink/agents/planning_agents/repo_loader.py
scilink/agents/planning_agents/scalarizer_agent.py
scilink/agents/planning_agents/user_interface.py
scilink/agents/planning_agents/__pycache__/__init__.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/_deprecation.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/base_agent.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/bo_agent.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/excel_parser.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/html_generator.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/ingestor.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/instruct.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/knowledge_base.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/orchestrator_tools.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/parser_utils.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/pdf_parser.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/planning_agent.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/planning_orchestrator.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/rag_engine.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/repo_loader.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/scalarizer_agent.cpython-312.pyc
scilink/agents/planning_agents/__pycache__/user_interface.cpython-312.pyc
scilink/agents/sim_agents/__init__.py
scilink/agents/sim_agents/_deprecation.py
scilink/agents/sim_agents/atomate2_utils.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/packmol_agent.py
scilink/agents/sim_agents/structure_agent.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_updater.py
scilink/agents/sim_agents/docs/aimsgb.txt
scilink/cli/__init__.py
scilink/cli/analyze.py
scilink/cli/main.py
scilink/cli/plan.py
scilink/cli/prepare_ff.py
scilink/cli/serve.py
scilink/cli/simulate.py
scilink/cli/ui.py
scilink/cli/__pycache__/__init__.cpython-312.pyc
scilink/cli/__pycache__/analyze.cpython-312.pyc
scilink/cli/__pycache__/main.cpython-312.pyc
scilink/cli/__pycache__/plan.cpython-312.pyc
scilink/cli/__pycache__/prepare_ff.cpython-312.pyc
scilink/cli/__pycache__/serve.cpython-312.pyc
scilink/cli/__pycache__/simulate.cpython-312.pyc
scilink/cli/__pycache__/ui.cpython-312.pyc
scilink/skills/__init__.py
scilink/skills/loader.py
scilink/skills/__pycache__/__init__.cpython-312.pyc
scilink/skills/__pycache__/loader.cpython-312.pyc
scilink/skills/curve_fitting/__init__.py
scilink/skills/curve_fitting/xps.md
scilink/skills/force_field/amber.md
scilink/skills/hyperspectral/__init__.py
scilink/skills/hyperspectral/eels.md
scilink/skills/image_analysis/__init__.py
scilink/skills/image_analysis/atomic_stem.md
scilink/skills/image_analysis/overlapping_objects.md
scilink/skills/planning/__init__.py
scilink/tools/amber_tools.py
scilink/tools/atom_finding_tools.py
scilink/tools/atomistic_model_manager.py
scilink/tools/atomistic_tools.py
scilink/tools/bo_tools.py
scilink/tools/curve_fitting_tools.py
scilink/tools/fft_nmf.py
scilink/tools/hyperspectral_tools.py
scilink/tools/image_analysis_tools.py
scilink/tools/image_processor.py
scilink/tools/particle_analyzer.py
scilink/tools/sam.py
scilink/tools/spectral_unmixer.py
scilink/tools/__pycache__/atom_finding_tools.cpython-312.pyc
scilink/tools/__pycache__/atomistic_tools.cpython-312.pyc
scilink/tools/__pycache__/bo_tools.cpython-312.pyc
scilink/tools/__pycache__/curve_fitting_tools.cpython-312.pyc
scilink/tools/__pycache__/fft_nmf.cpython-312.pyc
scilink/tools/__pycache__/hyperspectral_tools.cpython-312.pyc
scilink/tools/__pycache__/image_analysis_tools.cpython-312.pyc
scilink/tools/__pycache__/image_processor.cpython-312.pyc
scilink/tools/__pycache__/particle_analyzer.cpython-312.pyc
scilink/tools/__pycache__/sam.cpython-312.pyc
scilink/tools/__pycache__/spectral_unmixer.cpython-312.pyc
scilink/ui/__init__.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/__pycache__/__init__.cpython-312.pyc
scilink/ui/__pycache__/config.cpython-312.pyc
scilink/ui/__pycache__/output_capture.cpython-312.pyc
scilink/ui/__pycache__/state.cpython-312.pyc
scilink/ui/__pycache__/theme.cpython-312.pyc
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/file_viewer.py
scilink/ui/components/sidebar.py
scilink/ui/components/skills.py
scilink/ui/components/tools_agents.py
scilink/ui/components/__pycache__/__init__.cpython-312.pyc
scilink/ui/components/__pycache__/chat_uploads.cpython-312.pyc
scilink/ui/components/__pycache__/file_viewer.cpython-312.pyc
scilink/ui/components/__pycache__/sidebar.cpython-312.pyc
scilink/ui/components/__pycache__/skills.cpython-312.pyc
scilink/ui/components/__pycache__/tools_agents.cpython-312.pyc
scilink/workflows/__init__.py
scilink/workflows/analyzers.py
scilink/workflows/dft_recommendation_workflow.py
scilink/workflows/dft_workflow.py
scilink/workflows/experiment2dft.py
scilink/workflows/experiment_novelty_workflow.py
scilink/workflows/hyperspectral_analysis_workflow.py
scilink/workflows/md_workflow.py
scilink/workflows/microscopy_analysis_workflow.py
scilink/workflows/multimodal_workflow.py
scilink/workflows/spectroscopy1d_analysis_workflow.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
scilink/wrappers/__pycache__/__init__.cpython-312.pyc
scilink/wrappers/__pycache__/litellm_wrapper.cpython-312.pyc
scilink/wrappers/__pycache__/openai_wrapper.cpython-312.pyc
scilink/wrappers/__pycache__/openai_wrapper_embeddings.cpython-312.pyc
test_adaptive_annealing_data/dbg/scripts/fitting_script.py
test_adaptive_annealing_data/dbg2/scripts/fitting_script.py
test_adaptive_annealing_data/output_components/scripts/fitting_script.py
test_adaptive_annealing_data/output_easy/scripts/fitting_script.py
test_adaptive_annealing_data/output_emg/scripts/fitting_script.py
test_adaptive_annealing_data/output_hard/scripts/fitting_script.py
test_adaptive_annealing_data/output_overlap/scripts/fitting_script.py
test_adaptive_annealing_data/output_series/trend_analysis.py
test_adaptive_annealing_data/output_series/scripts/spectrum_0000.py
test_adaptive_annealing_data/output_series/scripts/spectrum_0001.py
test_adaptive_annealing_data/output_series/scripts/spectrum_0002.py
test_adaptive_annealing_data/output_series/scripts/spectrum_0003.py
test_adaptive_annealing_data/output_series/scripts/spectrum_0004.py
test_adaptive_annealing_data/output_stress/scripts/fitting_script.py
test_annealing_data/out_components/scripts/fitting_script.py
test_annealing_data/out_easy/scripts/fitting_script.py
test_annealing_data/out_hard/scripts/fitting_script.py
test_annealing_data/out_shape/scripts/fitting_script.py
test_annealing_data/out_skill/scripts/fitting_script.py
test_annealing_data/output/scripts/fitting_script.py
test_annealing_data/output_components/scripts/fitting_script.py
test_image_annealing_data/output/scripts/analysis_script.py
test_image_annealing_data/output/tier1/scripts/analysis_script.py
test_image_annealing_data/output_escalation/scripts/analysis_script.py
test_image_annealing_data/output_high_threshold/scripts/analysis_script.py
test_image_annealing_data/output_high_threshold/tier1/scripts/analysis_script.py
test_regime_data/output/trend_analysis.py
test_regime_data/output/scripts/spectrum_300K.py
test_regime_data/output/scripts/spectrum_350K.py
test_regime_data/output/scripts/spectrum_400K.py
test_regime_data/output/scripts/spectrum_450K.py
test_regime_data/output/scripts/spectrum_500K.py
test_series_annealing_data/o3/trend_analysis.py
test_series_annealing_data/o3/scripts/s0.py
test_series_annealing_data/o3/scripts/s1.py
test_series_annealing_data/o3/scripts/s2.py
test_series_annealing_data/out/trend_analysis.py
test_series_annealing_data/out/scripts/spec_0.py
test_series_annealing_data/out/scripts/spec_1.py
test_series_annealing_data/out/scripts/spec_2.py
test_series_annealing_data/output_series/trend_analysis.py
test_series_annealing_data/output_series/scripts/spectrum_0.py
test_series_annealing_data/output_series/scripts/spectrum_1.py
test_series_annealing_data/output_series/scripts/spectrum_2.py
test_series_annealing_data/output_series/scripts/spectrum_3.py
test_series_annealing_data/output_series/scripts/spectrum_4.py
test_series_data/output/trend_analysis.py
test_series_data/output/scripts/spectrum_300K.py
test_series_data/output/scripts/spectrum_350K.py
test_series_data/output/scripts/spectrum_400K.py
test_series_data/output/scripts/spectrum_450K.py
test_series_data/output/scripts/spectrum_500K.py
test_tier2_handoff/scripts/analysis_script.py
test_tier2_handoff/tier1/scripts/analysis_script.py
test_tier2_output/scripts/analysis_script.py
test_tier2_output_eutectic/scripts/analysis_script.py
test_tier2_output_eutectic/tier1/scripts/analysis_script.py
test_validator_data/v_baseline/scripts/fitting_script.py
test_validator_data/v_noconflict/scripts/fitting_script.py
test_validator_data/v_noplot/scripts/fitting_script.py
test_validator_data/v_obvious/scripts/fitting_script.py
test_validator_data/v_subtle/scripts/fitting_script.py
test_ybco_output/scripts/analysis_script.py
test_ybco_output/tier1/scripts/analysis_script.py
tests/test_adaptive_annealing.py
tests/test_adaptive_annealing_image.py
tests/test_bo_convergence.py
tests/test_hyperspectral_pipeline.py
tests/test_knowledge_query.py
tests/test_planning_campaigns.py
tests/test_preprocessing_orchestrator.py
tests/test_amber_skill/test_agent_amber_pipeline.py
tests/test_amber_skill/test_amber_tools.py
tests/test_amber_skill/test_skill_loading.py
tier2_test_results/scripts/analysis_script.py
tier2_test_results/tier1/scripts/analysis_script.py