n_parallel_clusters support and deps update

[parashardhapola]

PR Type

Enhancement, Other

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Description

• Add n_parallel_clusters parameter for concurrent model requests

• Update dependencies and version bump to 0.10.0

• Improve error handling for empty API responses

• Add input validation using Pydantic models

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Diagram Walkthrough

flowchart LR
  A["User Input"] --> B["Input Validation"]
  B --> C["Submit Job with n_parallel_clusters"]
  C --> D["API Processing"]
  D --> E["Poll Results with Error Handling"]

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File Walkthrough

	Relevant files
Miscellaneous	__init__.py Version bump to 0.10.0                                                                      cytetype/init.py Bump version from 0.9.2 to 0.10.0 +1/-1
Error handling	client.py Improve API error handling                                                              cytetype/client.py Add error handling for empty API responses Raise CyteTypeAPIError when no response received +2/-0
Enhancement	main.py Add parallel processing and input validation                          cytetype/main.py Add n_parallel_clusters parameter to run method Add input validation using Pydantic models Import InputData schema for validation Refactor LLM config validation logic +21/-2    server_schema.py Add parallel clusters schema field                                              cytetype/server_schema.py Add nParallelClusters field to InputData model Set constraints: minimum 1, maximum 50, default 2 Update example data with parallel clusters value +7/-0
Dependencies	pyproject.toml Update project dependencies                                                            pyproject.toml Update anndata dependency from ~0.11.4 to >=0.9.2 Update requests from ~2.32.3 to ~2.32.5 Update all dev dependencies to latest versions Change mypy Python version from 3.12 to 3.11 +9/-9

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[qodo-code-review]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review ValidationError import The code catches ValidationError but there is no added import for it in the diff. Ensure ValidationError is imported from pydantic to avoid NameError at runtime. try: input_data = InputData(**input_data).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 Payload construction The submit_job payload uses a conditional inline for llm_configs that may serialize to a malformed dict; double-check the resulting structure matches the server API (key present with list or omitted) and that empty lists are handled as intended. job_id = submit_job( { "input_data": input_data, "llm_configs": llm_configs if llm_configs else None, }, Error specificity On empty raw_response, a generic CyteTypeAPIError "No response from API" is raised; consider including job_id or status to aid debugging and avoid masking transient 'not_found' scenarios. if not raw_response: raise CyteTypeAPIError("No response from API") current_cluster_status = raw_response.get("clusterStatus", {})

[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
High-level	Loosening the anndata dependency is risky The anndata dependency constraint was loosened from ~=0.11.4 to >=0.9.2. This change is risky due to potential breaking changes in older anndata versions and could cause compatibility issues. Examples: pyproject.toml [8] "anndata>=0.9.2", Solution Walkthrough: Before: # pyproject.toml ... dependencies = [ "anndata~=0.11.4", # Restricts to versions >=0.11.4 and <0.12.0 ... ] ... After: # pyproject.toml ... dependencies = [ "anndata>=0.9.2", # Allows any version from 0.9.2 upwards ... ] ... Suggestion importance[1-10]: 8 __ Why: This suggestion correctly identifies a significant risk in loosening the anndata dependency, which could break the package for users with older versions and is a critical stability concern.	Medium
General	Remove redundant exception handling blocks Remove the redundant try...except blocks that catch, log, and then re-raise ValidationError, and instead allow the exception to propagate up the call stack. cytetype/main.py [315-328] -try: - input_data = InputData(**input_data).model_dump() -except ValidationError as e: - logger.error(f"Validation error: {e}") - raise e +# Let Pydantic's ValidationError propagate naturally. +input_data = InputData(**input_data).model_dump() 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 + llm_configs = [LLMModelConfig(**x).model_dump() for x in llm_configs] else: llm_configs = [] Apply / Chat Suggestion importance[1-10]: 5 __ Why: The suggestion correctly identifies a "log and re-raise" anti-pattern, and removing it simplifies the code and improves the error handling strategy.	Low
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