comprehensive support for SCFM (Single Cell Foundation Model) workflows in the CLI and REPL, enabling foundation model-based single-cell analysis#28
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HendricksJudy merged 6 commits intoaristoteleo:mainfrom Feb 13, 2026
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…l support Add /bio scfm command routing to pantheon-cli with init, run, and list_models subcommands. Includes workflow prompt template supporting scGPT, scBERT, Geneformer, scFoundation, and UCE models. 18 tests verify routing, prompt generation, integration with existing handlers, and command map registration. https://claude.ai/code/session_01WJcK8Jbk1ySamhGr5W1Gxg
…i-Y9Fe6 feat(scfm): add SCFM router and tests for Single Cell Foundation Mode…
Enable users to pass custom analysis goals via --question when running SCFM through the Pantheon CLI, ensuring the LLM tailors model selection, preprocessing and evaluation to the user's specific question. https://claude.ai/code/session_01WJcK8Jbk1ySamhGr5W1Gxg
…i-Y9Fe6 feat(scfm): add --question flag for user prompts in SCFM workflow
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Added Natural Language to Tool Mapping Guide
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This pull request introduces comprehensive support for SCFM (Single Cell Foundation Model) workflows in the CLI and REPL, enabling foundation model-based single-cell analysis. It adds a new prompt generator, expands the REPL command routing, updates help and suggestions, and includes robust test coverage for the new functionality.
SCFM Workflow Integration:
scfm_workflow.pyprompt generator for SCFM analysis, supporting multiple foundation models (scGPT, scBERT, Geneformer, scFoundation, UCE) and user analysis goals. (pantheon_cli/cli/prompt/scfm_workflow.py)/bio scfmcommand routing in the REPL, including subcommands forinit,run, andlist_models, with detailed help and model selection logic. (pantheon_cli/repl/bio_handler.py) [1] [2]User Experience Improvements:
pantheon_cli/repl/bio_handler.py) [1] [2]Command Mapping:
BIO_COMMAND_MAPfor proper routing and integration with the existing command system. (pantheon_cli/repl/bio_handler.py)Testing:
tests/test_scfm_router.py)