aiagents4pharma 1.25.1__tar.gz → 1.26.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/PKG-INFO +91 -29
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/README.md +90 -28
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma.egg-info/PKG-INFO +91 -29
- aiagents4pharma-1.26.0/release_version.txt +1 -0
- aiagents4pharma-1.25.1/release_version.txt +0 -1
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/LICENSE +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/configs/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/configs/config.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/states/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/tests/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/kegg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/ols.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/uniprot.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/config.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/models/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/models/basico_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/models/sys_bio_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/states/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_api.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_ask_question.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_basico_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_integration.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_param_scan.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_query_article.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_search_models.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_simulate_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_steady_state.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/ask_question.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/custom_plotter.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/get_annotation.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/load_arguments.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/load_biomodel.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/parameter_scan.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/query_article.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/search_models.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/simulate_model.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/steady_state.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tools/utils.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/agents/scp_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/states/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/states/state_talk2cells.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/tools/scp_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/states/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_summarization.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_nim_molmim.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/nim_molmim.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/ollama.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/agents/main_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/agents/s2_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/agents/zotero_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/app/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/config.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/search/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/search/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/state/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/state/state_talk2scholars.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_call_s2.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_call_zotero.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_main_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_routing_logic.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_s2_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_s2_tools.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_state.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_zotero_agent.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tests/test_zotero_tool.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/display_results.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/query_results.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/search.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/zotero/__init__.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma.egg-info/SOURCES.txt +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma.egg-info/dependency_links.txt +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma.egg-info/requires.txt +0 -0
- {aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma.egg-info/top_level.txt +0 -0
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## Feedback
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Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `
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Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀
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```plaintext
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OPENAI_API_KEY=your_openai_api_key
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# Notes:
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# - The API endpoint for Ollama is already set in env.example.
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# - Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
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# - Langsmith API for tracing is optional for both, set it in env.example if required.
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```
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To start the containers, run the following command:
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```sh
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docker compose --profile amd up # for AMD mode
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```
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This will:
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- Pull the latest images if they are not already available.
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- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network.
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- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs.
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To Access the web app, open your browser and go to:
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```
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http://localhost:8501
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```
|
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+
|
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+
To stop the containers, run:
|
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+
|
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+
```sh
|
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+
docker compose down
|
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+
```
|
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+
|
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+
##### **Run Talk2Biomodels and Talk2Scholars**
|
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+
|
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+
1. **Run the containers**
|
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|
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```bash
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docker run -d \
|
@@ -69,8 +124,8 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
|
|
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virtualpatientengine/talk2scholars
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|
```
|
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126
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|
72
|
-
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73
|
-
|
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+
2. **Access the Web App**
|
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+
Open your browser and go to:
|
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|
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|
```
|
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|
http://localhost:8501
|
@@ -96,36 +151,43 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
|
|
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cd AIAgents4Pharma
|
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```
|
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|
2. **Install dependencies:**
|
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+
|
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```bash
|
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pip install -r requirements.txt
|
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|
```
|
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-
|
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+
|
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+
⚠️ The current version of T2KG requires additional Ollama library to be installed.
|
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|
|
104
161
|
Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download)
|
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|
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|
As an alternative, use the following commands to install the library using terminal and to pull necessary model:
|
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|
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- Ubuntu:
|
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-
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110
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-
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111
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-
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-
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+
```
|
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+
curl -fsSL https://ollama.com/install.sh | sh
|
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ollama pull nomic-embed-text
|
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+
```
|
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|
- Windows:
|
114
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-
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-
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-
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-
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-
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-
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+
```
|
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+
curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
|
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+
tar -xzf .\ollama-windows-amd64.zip
|
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|
+
start ollama serve
|
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|
+
ollama pull nomic-embed-text
|
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|
+
```
|
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177
|
- macOS:
|
121
|
-
|
122
|
-
|
123
|
-
|
124
|
-
|
125
|
-
|
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|
+
```
|
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|
+
brew install ollama
|
180
|
+
ollama pull nomic-embed-text
|
181
|
+
```
|
182
|
+
A list of pulled Ollama models can be checked using the following command:
|
183
|
+
|
126
184
|
```
|
127
185
|
ollama list
|
128
186
|
```
|
187
|
+
|
188
|
+
⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed.
|
189
|
+
You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
|
190
|
+
|
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|
3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
|
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|
|
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|
```bash
|
@@ -195,4 +257,4 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
|
|
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|
|
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|
## Feedback
|
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|
|
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|
-
Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `
|
260
|
+
Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀
|
@@ -1,6 +1,6 @@
|
|
1
1
|
Metadata-Version: 2.2
|
2
2
|
Name: aiagents4pharma
|
3
|
-
Version: 1.
|
3
|
+
Version: 1.26.0
|
4
4
|
Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
|
5
5
|
Classifier: Programming Language :: Python :: 3
|
6
6
|
Classifier: License :: OSI Approved :: MIT License
|
@@ -67,6 +67,7 @@ Requires-Dist: scanpy==1.11.0
|
|
67
67
|
[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
|
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|
[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
|
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|
[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
|
70
|
+
[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
|
70
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|

|
71
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|

|
72
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|

|
@@ -97,23 +98,77 @@ Our toolkit currently consists of the following agents:
|
|
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|
pip install aiagents4pharma
|
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|
```
|
99
100
|
|
100
|
-
Check out the tutorials on each agent for detailed
|
101
|
+
Check out the tutorials on each agent for detailed instructions.
|
101
102
|
|
102
103
|
#### Option 2: Docker Hub
|
103
104
|
|
104
|
-
|
105
|
+
_We now have `Talk2AIAgents4Pharma`, `Talk2Biomodels`, and `Talk2Scholars` available on Docker Hub._
|
105
106
|
|
106
|
-
|
107
|
+
##### **Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs**
|
107
108
|
|
108
|
-
|
109
|
-
docker pull virtualpatientengine/talk2biomodels
|
110
|
-
```
|
109
|
+
Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network.
|
111
110
|
|
112
|
-
|
113
|
-
|
111
|
+
###### **Setup Environment Variables**
|
112
|
+
|
113
|
+
1. Choose the app you want to use:
|
114
|
+
|
115
|
+
```sh
|
116
|
+
# Navigate to the correct directory before setting up environment variables.
|
117
|
+
# Use one of the following commands based on the agent you want to use:
|
118
|
+
cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma
|
119
|
+
cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs
|
120
|
+
```
|
121
|
+
|
122
|
+
2. Copy the `.env.example` file and rename it to `.env`:
|
123
|
+
```sh
|
124
|
+
cp .env.example .env
|
114
125
|
```
|
126
|
+
3. Open the `.env` file and add your API keys:
|
127
|
+
|
128
|
+
```plaintext
|
129
|
+
OPENAI_API_KEY=your_openai_api_key
|
130
|
+
NVIDIA_API_KEY=your_nvidia_api_key
|
131
|
+
OLLAMA_HOST=http://ollama:11434
|
132
|
+
LANGCHAIN_TRACING_V2=true
|
133
|
+
LANGCHAIN_API_KEY=your_langchain_api_key_here
|
134
|
+
# Notes:
|
135
|
+
# - The API endpoint for Ollama is already set in env.example.
|
136
|
+
# - Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
|
137
|
+
# - If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
|
138
|
+
# - Langsmith API for tracing is optional for both, set it in env.example if required.
|
139
|
+
```
|
140
|
+
|
141
|
+
4. Save the file.
|
142
|
+
|
143
|
+
To start the containers, run the following command:
|
144
|
+
|
145
|
+
```sh
|
146
|
+
docker compose --profile cpu up # for CPU mode
|
147
|
+
docker compose --profile nvidia up # for GPU mode
|
148
|
+
docker compose --profile amd up # for AMD mode
|
149
|
+
```
|
150
|
+
|
151
|
+
This will:
|
152
|
+
|
153
|
+
- Pull the latest images if they are not already available.
|
154
|
+
- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network.
|
155
|
+
- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs.
|
115
156
|
|
116
|
-
|
157
|
+
To Access the web app, open your browser and go to:
|
158
|
+
|
159
|
+
```
|
160
|
+
http://localhost:8501
|
161
|
+
```
|
162
|
+
|
163
|
+
To stop the containers, run:
|
164
|
+
|
165
|
+
```sh
|
166
|
+
docker compose down
|
167
|
+
```
|
168
|
+
|
169
|
+
##### **Run Talk2Biomodels and Talk2Scholars**
|
170
|
+
|
171
|
+
1. **Run the containers**
|
117
172
|
|
118
173
|
```bash
|
119
174
|
docker run -d \
|
@@ -134,8 +189,8 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
|
|
134
189
|
virtualpatientengine/talk2scholars
|
135
190
|
```
|
136
191
|
|
137
|
-
|
138
|
-
|
192
|
+
2. **Access the Web App**
|
193
|
+
Open your browser and go to:
|
139
194
|
|
140
195
|
```
|
141
196
|
http://localhost:8501
|
@@ -161,36 +216,43 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
|
|
161
216
|
cd AIAgents4Pharma
|
162
217
|
```
|
163
218
|
2. **Install dependencies:**
|
219
|
+
|
164
220
|
```bash
|
165
221
|
pip install -r requirements.txt
|
166
222
|
```
|
167
|
-
|
223
|
+
|
224
|
+
⚠️ The current version of T2KG requires additional Ollama library to be installed.
|
168
225
|
|
169
226
|
Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download)
|
170
227
|
|
171
228
|
As an alternative, use the following commands to install the library using terminal and to pull necessary model:
|
172
229
|
|
173
230
|
- Ubuntu:
|
174
|
-
|
175
|
-
|
176
|
-
|
177
|
-
|
231
|
+
```
|
232
|
+
curl -fsSL https://ollama.com/install.sh | sh
|
233
|
+
ollama pull nomic-embed-text
|
234
|
+
```
|
178
235
|
- Windows:
|
179
|
-
|
180
|
-
|
181
|
-
|
182
|
-
|
183
|
-
|
184
|
-
|
236
|
+
```
|
237
|
+
curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
|
238
|
+
tar -xzf .\ollama-windows-amd64.zip
|
239
|
+
start ollama serve
|
240
|
+
ollama pull nomic-embed-text
|
241
|
+
```
|
185
242
|
- macOS:
|
186
|
-
|
187
|
-
|
188
|
-
|
189
|
-
|
190
|
-
|
243
|
+
```
|
244
|
+
brew install ollama
|
245
|
+
ollama pull nomic-embed-text
|
246
|
+
```
|
247
|
+
A list of pulled Ollama models can be checked using the following command:
|
248
|
+
|
191
249
|
```
|
192
250
|
ollama list
|
193
251
|
```
|
252
|
+
|
253
|
+
⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed.
|
254
|
+
You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
|
255
|
+
|
194
256
|
3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
|
195
257
|
|
196
258
|
```bash
|
@@ -260,4 +322,4 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
|
|
260
322
|
|
261
323
|
## Feedback
|
262
324
|
|
263
|
-
Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `
|
325
|
+
Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀
|
@@ -0,0 +1 @@
|
|
1
|
+
v1.26.0
|
@@ -1 +0,0 @@
|
|
1
|
-
v1.25.1
|
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2aiagents4pharma/__init__.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/__init__.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/agents/__init__.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/__init__.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/kegg.py
RENAMED
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/api/uniprot.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/__init__.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/configs/config.yaml
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/models/__init__.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/states/__init__.py
RENAMED
File without changes
|
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/__init__.py
RENAMED
File without changes
|
{aiagents4pharma-1.25.1 → aiagents4pharma-1.26.0}/aiagents4pharma/talk2biomodels/tests/test_api.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|