How do I include external tool tests in my run?

You can trigger external tool tests by setting the environment variable MYCELIA_RUN_EXTERNAL=true before executing the Julia test command.

What is the primary purpose of the Mycelia Test Stages skill?

It provides a standardized framework for organizing and running tests in the Mycelia project, ensuring that complex biological analysis workflows are tested in logical, tiered stages.

Does this skill support code coverage reporting?

Yes, it provides specific commands to run the full pipeline with coverage enabled, including flags to disable precompilation for accurate line-hit reporting.

Why does this skill enforce the use of StableRNGs?

StableRNGs are used to provide deterministic seeds for random number generation, which is critical for making biological data tests reproducible across different environments.

Mycelia Test Stage Manager

Name: Mycelia Test Stage Manager
Author: cjprybol

bycjprybol

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Security & Testing

Organizes and executes multi-stage testing workflows for Mycelia multiomic analysis and biological data pipelines.

About

The Mycelia Test Stage Manager is a specialized skill designed to navigate and maintain the complex, tiered testing architecture of the Mycelia project. It provides structured guidance for an 8-stage testing suite—covering everything from data acquisition to pangenomics—while enforcing best practices like deterministic randomness with StableRNGs and environment-gated external tool testing. This skill is essential for developers working on high-performance biological characterization tools who need to ensure reliability across data-intensive bioinformatics workflows.

Key Features

Tiered 8-stage test organization for modular bioinformatics validation
Standardized test fixture and directory naming conventions
6 GitHub stars
Integration with StableRNGs for deterministic and reproducible test results
Environment-gated testing for external tools and full pipeline execution
Static analysis support using JET and Aqua for Julia code quality

Use Cases

Validating new bioinformatics tool integrations within the Mycelia ecosystem
Running high-coverage CI/CD pipelines for multiomic data processing
Ensuring deterministic behavior in stochastic biological simulations

About

Key Features

Tiered 8-stage test organization for modular bioinformatics validation
Standardized test fixture and directory naming conventions
6 GitHub stars
Integration with StableRNGs for deterministic and reproducible test results
Environment-gated testing for external tools and full pipeline execution
Static analysis support using JET and Aqua for Julia code quality

Use Cases

Validating new bioinformatics tool integrations within the Mycelia ecosystem
Running high-coverage CI/CD pipelines for multiomic data processing
Ensuring deterministic behavior in stochastic biological simulations