feat(phenograph_clustering_template): add phenograph_clustering_templ…

[fangliu117]

…ate function and unit tests

[Copilot]

Pull Request Overview

This PR introduces a new Phenograph clustering template with platform-agnostic functionality converted from NIDAP, including both the main template function and comprehensive unit tests.

• Implements phenograph_clustering_template with JSON parameter parsing and flexible I/O handling
• Adds comprehensive unit tests covering I/O workflows, parameter validation, and function mocking
• Provides CLI interface for standalone execution

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/spac/templates/phenograph_clustering_template.py	Main template implementation with JSON parameter parsing, clustering execution, and flexible save/return options
tests/templates/test_phenograph_clustering_template.py	Comprehensive unit tests with mock data generation, I/O testing, and parameter validation

Comments suppressed due to low confidence (5)

src/spac/templates/phenograph_clustering_template.py:57

• Variable name Layer_name uses inconsistent PascalCase naming. Should be layer_name to follow Python naming conventions.

    Layer_name = params.get("Table_to_Process", "Original")

src/spac/templates/phenograph_clustering_template.py:58

• Variable name K_cluster uses inconsistent PascalCase naming. Should be k_cluster to follow Python naming conventions.

    K_cluster = params.get("K_Nearest_Neighbors", 30)

src/spac/templates/phenograph_clustering_template.py:59

• Variable name Seed uses inconsistent PascalCase naming. Should be seed to follow Python naming conventions.

    Seed = params.get("Seed", 42)

src/spac/templates/phenograph_clustering_template.py:80

• Using PascalCase variable K_cluster inconsistent with Python naming conventions. Should use k_cluster.

        k=K_cluster,

src/spac/templates/phenograph_clustering_template.py:81

• Using PascalCase variable Seed inconsistent with Python naming conventions. Should use seed.

        seed=Seed,