SCMCP

Instructions

Implementation Reference

• src/scmcp/tool/tl.py:47-52 (registration)

  MCP tool registration for 'leiden' with name, description, and schema reference.
  # Add leiden tool leiden_tool = types.Tool( name="leiden", description="Leiden clustering algorithm for community detection", inputSchema=LeidenModel.model_json_schema(), )
• src/scmcp/schema/tl.py:267-342 (schema)

  Pydantic model defining input schema and validation for leiden tool parameters.
  class LeidenModel(JSONParsingModel): """Input schema for the Leiden clustering algorithm.""" resolution: float = Field( default=1.0, description="A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters." ) random_state: int = Field( default=0, description="Change the initialization of the optimization." ) key_added: str = Field( default='leiden', description="`adata.obs` key under which to add the cluster labels." ) directed: Optional[bool] = Field( default=None, description="Whether to treat the graph as directed or undirected." ) use_weights: bool = Field( default=True, description="If `True`, edge weights from the graph are used in the computation (placing more emphasis on stronger edges)." ) n_iterations: int = Field( default=-1, description="How many iterations of the Leiden clustering algorithm to perform. -1 runs until optimal clustering." ) neighbors_key: Optional[str] = Field( default=None, description="Use neighbors connectivities as adjacency. If specified, leiden looks .obsp[.uns[neighbors_key]['connectivities_key']] for connectivities." ) obsp: Optional[str] = Field( default=None, description="Use .obsp[obsp] as adjacency. You can't specify both `obsp` and `neighbors_key` at the same time." ) flavor: Literal['leidenalg', 'igraph'] = Field( default='igraph', description="Which package's implementation to use." ) clustering_args: Optional[Dict[str, Any]] = Field( default=None, description="Any further arguments to pass to the clustering algorithm." ) @field_validator('resolution') def validate_resolution(cls, v: float) -> float: """Validate resolution is positive""" if v <= 0: raise ValueError("resolution must be a positive number") return v @field_validator('obsp', 'neighbors_key') def validate_graph_source(cls, v: Optional[str], info: ValidationInfo) -> Optional[str]: """Validate that obsp and neighbors_key are not both specified""" values = info.data if v is not None and 'obsp' in values and 'neighbors_key' in values: if values['obsp'] is not None and values['neighbors_key'] is not None: raise ValueError("Cannot specify both obsp and neighbors_key") return v @field_validator('flavor') def validate_flavor(cls, v: str) -> str: """Validate flavor is supported""" if v not in ['leidenalg', 'igraph']: raise ValueError("flavor must be either 'leidenalg' or 'igraph'") return v
• src/scmcp/tool/tl.py:164-177 (handler)

  Generic execution handler for tl tools including 'leiden'; resolves sc.tl.leiden from tl_func dict, validates parameters via signature, executes on active adata, and logs operation.
  def run_tl_func(ads, func, arguments): adata = ads.adata_dic[ads.active] if func not in tl_func: raise ValueError(f"Unsupported function: {func}") run_func = tl_func[func] parameters = inspect.signature(run_func).parameters kwargs = {k: arguments.get(k) for k in parameters if k in arguments} try: res = run_func(adata, **kwargs) add_op_log(adata, run_func, kwargs) except Exception as e: logger.error(f"Error running function {func}: {e}") raise return
• src/scmcp/tool/tl.py:125-142 (helper)

  Mapping dictionary tl_func that associates 'leiden' tool name with scanpy.tl.leiden function for execution.
  tl_func = { "tsne": sc.tl.tsne, "umap": sc.tl.umap, "draw_graph": sc.tl.draw_graph, "diffmap": sc.tl.diffmap, "embedding_density": sc.tl.embedding_density, "leiden": sc.tl.leiden, "louvain": sc.tl.louvain, "dendrogram": sc.tl.dendrogram, "dpt": sc.tl.dpt, "paga": sc.tl.paga, "ingest": sc.tl.ingest, "rank_genes_groups": sc.tl.rank_genes_groups, "filter_rank_genes_groups": sc.tl.filter_rank_genes_groups, "marker_gene_overlap": sc.tl.marker_gene_overlap, "score_genes": sc.tl.score_genes, "score_genes_cell_cycle": sc.tl.score_genes_cell_cycle, }
• src/scmcp/tool/tl.py:145-162 (helper)

  tl_tools dictionary that includes the 'leiden' tool object for listing and dispatch.
  tl_tools = { "tsne": tsne_tool, "umap": umap_tool, "draw_graph": draw_graph_tool, "diffmap": diffmap_tool, "embedding_density": embedding_density_tool, "leiden": leiden_tool, "louvain": louvain_tool, "dendrogram": dendrogram_tool, "dpt": dpt_tool, "paga": paga_tool, "ingest": ingest_tool, "rank_genes_groups": rank_genes_groups_tool, "filter_rank_genes_groups": filter_rank_genes_groups_tool, "marker_gene_overlap": marker_gene_overlap_tool, "score_genes": score_genes_tool, "score_genes_cell_cycle": score_genes_cell_cycle_tool, }