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Quick Start Guide

Setup

# Create and activate virtual environment
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install dependencies
pip install -e .

Common Commands

Testing

# Run all tests
make test

# Run module tests
make modules-test

# Run specific module tests
cd modules/Clinical && make test

# Run individual test file
python -m unittest modules/Clinical/tests/test_*.py -v

Schema Generation

# Generate schema classes for all modules
make modules-gen

# Generate schema classes for specific module
cd modules/Clinical && make gen-schema

Example Validation

# Validate examples
make test-examples

CI Testing

# Using act (GitHub Actions local runner)
act -l  # List workflows
act pull_request  # Run PR workflow

# Manual CI testing
python -m venv ci-venv
source ci-venv/bin/activate
pip install -e .
make test

Common Issues and Solutions

Tests Failing

  1. Check Python version (CI uses 3.10)
  2. Verify dependencies: pip install -e .
  3. Check environment variables

Schema Issues

  1. Regenerate schema: make modules-gen
  2. Check YAML syntax
  3. Verify required fields

Import Errors

  1. Check PYTHONPATH
  2. Verify package installation
  3. Check module structure

Project Structure

htan2-data-model/
├── modules/          # Module definitions
├── docs/            # Documentation
├── examples/        # Example data
├── src/            # Source code
└── Makefile        # Build rules

Getting Help

  • Check docs/development.md for detailed guide
  • Review GitHub issues
  • Contact maintainers