Skip to content

SPEC.md

Latest commit

 

History

History
77 lines (63 loc) · 2.81 KB

SPEC.md

File metadata and controls

77 lines (63 loc) · 2.81 KB

Specification: scripts

Scope

Executable scripts and utilities for running METAINFORMANT workflows. Contains thin wrapper orchestrators that invoke core library functions, package management tools, and utility scripts. Scripts are organized by domain module.

Architecture

  • Dependency Level: Orchestration
  • Component Type: Executable Scripts
  • Design Pattern: Thin Wrapper Orchestration

Directory Structure

scripts/
├── package/            # Package management and build scripts
│   ├── setup.sh        # Environment setup
│   ├── test.sh         # Test runner
│   ├── build.sh        # Package builder
│   └── uv_quality.sh   # Code quality checks
├── core/               # Core utility scripts
├── {module}/           # Domain-specific scripts
│   ├── run_workflow.py # Workflow orchestration
│   └── {feature}.py    # Feature-specific scripts
└── *.py                # Root-level utility scripts

Data Structures

Script Types

  • Workflow Scripts: Orchestrate multi-step pipelines (run_workflow.py, run_analysis.py)
  • Utility Scripts: Single-purpose tools (audit_docs.py, check_exports.py)
  • Package Scripts: Build, test, and quality tools (setup.sh, test.sh, build.sh)
  • Generation Scripts: Generate code, docs, or configs (generate_example.py, generate_specs.py)

Module Subdirectories

Each domain has a corresponding scripts subdirectory:

  • core/, dna/, rna/, gwas/, protein/, epigenome/
  • networks/, multiomics/, singlecell/, visualization/
  • quality/, ml/, math/, menu/, ontology/
  • phenotype/, ecology/, simulation/, life_events/

Package Scripts (scripts/package/)

Script Purpose
setup.sh Install development environment
test.sh Run pytest with various modes
build.sh Build distributable package
uv_quality.sh Run formatters, linters, type checkers
uv_docs.sh Build Sphinx documentation
validate_build.sh Verify build artifacts

Interface

Running Scripts

# Package management
bash scripts/package/setup.sh        # Setup environment
bash scripts/package/test.sh         # Run tests
bash scripts/package/uv_quality.sh   # Code quality

# Domain workflows
python scripts/rna/run_workflow.py --config config/amalgkit/species.yaml
uv run python scripts/gwas/run_analysis.py --config config/gwas/gwas.yaml

# Utilities
python scripts/generate_example.py --module dna --feature alignment
python scripts/audit_docs.py

Script Conventions

  • All scripts executable directly or via uv run
  • Use metainformant.core utilities for I/O and logging
  • Write all outputs to output/ directory
  • Support --help flag for argument documentation
  • Follow NO MOCKING policy (real implementations only)
  • Use argparse or click for CLI argument handling