n_parallel_clusters support and deps update

cytetype/__init__.py

@@ -1,4 +1,4 @@
 from .main import CyteType
 
 __all__ = ["CyteType"]
-__version__ = "0.9.2"
+__version__ = "0.10.0"

cytetype/client.py

@@ -154,6 +154,8 @@ def poll_for_results(
 
             # Extract cluster status for all cases
             raw_response = status_response.get("raw_response", {})
+            if not raw_response:
+                raise CyteTypeAPIError("No response from API")
             current_cluster_status = raw_response.get("clusterStatus", {})
 
             if status == "completed":

cytetype/main.py

@@ -1,14 +1,15 @@
-from typing import Any
+from typing import Any, cast
 import json
 
 import anndata
 import pandas as pd
 from natsort import natsorted
+from pydantic import ValidationError
 
 
 from .config import logger, DEFAULT_API_URL, DEFAULT_POLL_INTERVAL, DEFAULT_TIMEOUT
 from .client import submit_job, poll_for_results, check_job_status
-from .server_schema import LLMModelConfig
+from .server_schema import LLMModelConfig, InputData
 from .anndata_helpers import (
     _validate_adata,
     _calculate_pcent,
@@ -245,6 +246,7 @@ def run(
         study_context: str,
         llm_configs: list[dict[str, Any]] | None = None,
         metadata: dict[str, Any] | None = None,
+        n_parallel_clusters: int = 2,
         results_prefix: str = "cytetype",
         poll_interval_seconds: int = DEFAULT_POLL_INTERVAL,
         timeout_seconds: int = DEFAULT_TIMEOUT,
@@ -267,6 +269,8 @@ def run(
             metadata (dict[str, Any] | None, optional): Custom metadata tags to include in the report header.
                 Values that look like URLs will be made clickable in the report.
                 Defaults to None.
+            n_parallel_clusters (int, optional): Number of parallel requests to make to the model. Maximum is 50. Note than high values can lead to rate limit errors.
+                Defaults to 2.
             results_prefix (str, optional): Prefix for keys added to `adata.obs` and `adata.uns` to
                 store results. The final annotation column will be
                 `adata.obs[f"{results_key}_{group_key}"]`. Defaults to "cytetype".
@@ -306,8 +310,25 @@ def run(
             "markerGenes": self.marker_genes,
             "visualizationData": self.visualization_data,
             "expressionData": self.expression_percentages,
+            "nParallelClusters": n_parallel_clusters,
         }
 
+        try:
+            validated_input = InputData(**cast(dict[str, Any], input_data))
+            input_data = validated_input.model_dump()
+        except ValidationError as e:
+            logger.error(f"Validation error: {e}")
+            raise e
+
+        if llm_configs:
+            try:
+                llm_configs = [LLMModelConfig(**x).model_dump() for x in llm_configs]
+            except ValidationError as e:
+                logger.error(f"Validation error: {e}")
+                raise e
+        else:
+            llm_configs = []
+
         if save_query:
             with open(query_filename, "w") as f:
                 json.dump(input_data, f)
@@ -316,9 +337,7 @@ def run(
         job_id = submit_job(
             {
                 "input_data": input_data,
-                "llm_configs": [LLMModelConfig(**x).model_dump() for x in llm_configs]
-                if llm_configs
-                else None,
+                "llm_configs": llm_configs if llm_configs else None,
             },
             api_url,
             auth_token=auth_token,

cytetype/server_schema.py

@@ -83,6 +83,12 @@ class InputData(BaseModel):
         default_factory=dict,
         description="Dictionary mapping gene names to their expression percentages across clusters",
     )
+    nParallelClusters: int = Field(
+        default=2,
+        ge=1,
+        le=50,
+        description="Number of parallel requests to make to the model",
+    )
 
     @classmethod
     def get_example(cls) -> "InputData":
@@ -151,4 +157,5 @@ def get_example(cls) -> "InputData":
                     "Cluster3": 5.2,
                 },
             },
+            nParallelClusters=5,
         )

pyproject.toml

@@ -5,10 +5,10 @@ description = "Python client for characterization of clusters from single-cell R
 readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
-    "anndata~=0.11.4",
+    "anndata>=0.9.2",
     "loguru~=0.7.3",
     "natsort~=8.4.0",
-    "requests~=2.32.3",
+    "requests~=2.32.5",
     "pydantic~=2.11.7",
     "session-info~=1.0.1",
     "python-dotenv~=1.1.1",
@@ -26,12 +26,12 @@ Repository = "https://github.com/NygenAnalytics/cytetype"
 
 [dependency-groups]
 dev = [
-    "jupyterlab>=4.4.2",
-    "mypy>=1.15.0",
-    "pytest>=8.3.5",
-    "ruff>=0.11.7",
-    "scanpy>=1.11.1",
-    "types-requests>=2.32.0.20250328",
+    "jupyterlab>=4.4.6",
+    "mypy>=1.17.1",
+    "pytest>=8.4.1",
+    "ruff>=0.12.11",
+    "scanpy>=1.11.4",
+    "types-requests>=2.32.4.20250809",
 ]
 
 [build-system]
@@ -47,7 +47,7 @@ version = {attr = "cytetype.__version__"}
 [tool.mypy]
 strict = false
 
-python_version = "3.12"
+python_version = "3.11"
 
 disable_error_code = ["import-untyped"]