├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── compose.yaml ├── denario ├── __init__.py ├── cli.py ├── config.py ├── denario.py ├── experiment.py ├── idea.py ├── key_manager.py ├── langgraph_agents │ ├── __init__.py │ ├── agents_graph.py │ ├── idea.py │ ├── literature.py │ ├── methods.py │ ├── parameters.py │ ├── pdf_reader.py │ ├── prompts.py │ ├── reader.py │ ├── referee.py │ └── routers.py ├── llm.py ├── method.py ├── paper_agents │ ├── LaTeX │ │ ├── AAS_keywords.txt │ │ ├── JHEP.bst │ │ ├── aas_macros.sty │ │ ├── aasjournal.bst │ │ ├── aastex631.cls │ │ ├── fancyhdr.sty │ │ ├── icml2025.bst │ │ ├── icml2025.sty │ │ ├── jcappub.sty │ │ ├── neurips_2025.sty │ │ └── pasj01.cls │ ├── __init__.py │ ├── agents_graph.py │ ├── journal.py │ ├── latex.py │ ├── latex_presets.py │ ├── literature.py │ ├── paper_node.py │ ├── parameters.py │ ├── prompts.py │ ├── reader.py │ ├── routers.py │ └── tools.py ├── prompts │ ├── experiment.py │ ├── idea.py │ └── method.py ├── research.py └── utils.py ├── docker ├── Dockerfile.dev └── Dockerfile.prod ├── docs ├── Write_paper │ └── Project2 │ │ └── paper │ │ └── paper_v2_no_citations.pdf ├── api_ref │ ├── api_classes.md │ ├── api_denario.md │ ├── api_journals.md │ ├── api_llms.md │ ├── api_paper.md │ └── api_utils.md ├── app.md ├── css │ ├── extra.css │ └── mkdocstrings.css ├── docker.md ├── examples │ ├── EtE_Gemini_fast.ipynb │ ├── denario_oscillator_full_run.ipynb │ ├── enhance_input.ipynb │ ├── idea_check.ipynb │ ├── research_idea.ipynb │ └── write_paper.ipynb ├── get_started.md ├── index.md ├── install.md ├── llm_api_keys │ ├── apikeys.md │ ├── cost.md │ ├── obtaining-api-keys.md │ ├── storing-api-keys.md │ └── vertex-ai-setup.md ├── prompts.md ├── requirements.txt ├── resources.md ├── troubleshooting.md └── tutorials │ ├── tut_end2end.md │ ├── tut_gui.md │ ├── tut_install.md │ └── tut_llm_api.md ├── examples ├── GW231123 │ └── input.md ├── Project1 │ ├── input.md │ └── input_files │ │ └── idea.md ├── Project2 │ ├── input.md │ └── input_files │ │ ├── data_description.md │ │ ├── idea.md │ │ ├── methods.md │ │ ├── plots │ │ ├── boxplots_data_value_num_6_1749851184.png │ │ ├── boxplots_input_intendedretrievals_4_1749851184.png │ │ ├── boxplots_output_livebirths_5_1749851184.png │ │ ├── hist_efficiency_scores_1_1749851516.png │ │ ├── histograms_data_value_num_3_1749851184.png │ │ ├── histograms_input_intendedretrievals_1_1749851184.png │ │ ├── histograms_output_livebirths_2_1749851184.png │ │ ├── plot_temporal_mean_efficiency_4_1749851516.png │ │ ├── violin_efficiency_scores_2_1749851516.png │ │ └── violin_sensitivity_zero_outputs_3_1749851516.png │ │ └── results.md ├── enhance_input.ipynb ├── full_workflow.py ├── get_keywords.ipynb ├── idea_check.ipynb ├── oscillator_full_run.ipynb ├── research_idea.ipynb └── write_paper.ipynb ├── mkdocs.yml ├── pyproject.toml └── tests └── full_paper.py /.gitignore: -------------------------------------------------------------------------------- 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