├── .dockerignore ├── .github └── workflows │ └── test.yml ├── .gitignore ├── Dockerfile ├── MANIFEST.in ├── README.md ├── examples ├── data │ ├── GO_cafm.json │ ├── GO_cafm.tif │ ├── MoS2_stem_Exp-000-2.json │ ├── MoS2_stem_Exp-000-2.npy │ ├── MoS2_stem_Exp-001-5.json │ ├── MoS2_stem_Exp-001-5.npy │ ├── MoS2_stem_Exp-002-5.json │ ├── MoS2_stem_Exp-002-5.npy │ ├── YBCO_tem.json │ ├── YBCO_tem.tif │ ├── nanoparticles.json │ ├── nanoparticles.npy │ ├── tepl.json │ └── tepl.npy ├── dft_workflow.py ├── novelty_assesment_microscopy.py └── novelty_assesment_spectroscopy.py ├── misc ├── scilink-agents.jpg ├── scilink-logo.svg ├── scilink-workflows.jpg └── scilink_logo_v2.svg ├── pyproject.toml ├── requirements.txt └── scilink ├── __init__.py ├── agents ├── __init__.py ├── exp_agents │ ├── __init__.py │ ├── atomistic_microscopy_agent.py │ ├── base_agent.py │ ├── central_microscopy_agent.py │ ├── controllers │ │ ├── atomistic_controllers.py │ │ ├── base_controllers.py │ │ ├── curve_fitting_controllers.py │ │ ├── hyperspectral_controllers.py │ │ ├── microscopy_controllers.py │ │ └── sam_controllers.py │ ├── curve_fitting_agent.py │ ├── holistic_microscopy_agent.py │ ├── human_feedback.py │ ├── hyperspectral_analysis_agent.py │ ├── instruct.py │ ├── metadata_converter.py │ ├── microscopy_agent.py │ ├── orchestrator_agent.py │ ├── pipeline_registry.py │ ├── pipeline_selector.py │ ├── pipelines │ │ ├── atomistic_pipelines.py │ │ ├── curve_fitting_pipelines.py │ │ ├── hyperspectral_pipelines.py │ │ ├── microscopy_pipelines.py │ │ └── sam_pipelines.py │ ├── preprocess.py │ ├── recommendation_agent.py │ ├── sam_microscopy_agent.py │ └── utils.py ├── lit_agents │ ├── __init__.py │ ├── instruct.py │ ├── literature_agent.py │ └── novelty_scorer.py ├── planning_agents │ ├── __init__.py │ ├── excel_parser.py │ ├── instruct.py │ ├── knowledge_base.py │ ├── parser_utils.py │ ├── pdf_parser.py │ ├── planning_agent.py │ ├── rag_engine.py │ ├── repo_loader.py │ └── user_interface.py └── sim_agents │ ├── __init__.py │ ├── atomate2_utils.py │ ├── docs │ └── aimsgb.txt │ ├── force_field_agent.py │ ├── instruct.py │ ├── lammps_agent.py │ ├── lammps_updater.py │ ├── lammps_utils.py │ ├── llm_client.py │ ├── packmol_agent.py │ ├── structure_agent.py │ ├── tools.py │ ├── utils.py │ ├── val_agent.py │ ├── vasp_agent.py │ └── vasp_updater.py ├── auth.py ├── cli ├── __init__.py ├── agents.py ├── run_agent.py └── workflows.py ├── executors.py ├── tools ├── atomistic_model_manager.py ├── atomistic_tools.py ├── curve_fitting_tools.py ├── fft_nmf.py ├── hyperspectral_tools.py ├── image_processor.py ├── sam.py └── spectral_unmixer.py ├── workflows ├── __init__.py ├── analyzers.py ├── dft_recommendation_workflow.py ├── dft_workflow.py ├── experiment2dft.py ├── experiment_novelty_workflow.py ├── hyperspectral_analysis_workflow.py ├── md_workflow.py ├── microscopy_analysis_workflow.py ├── multimodal_workflow.py └── spectroscopy1d_analysis_workflow.py └── wrappers 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