Comprehensive Test Suite for ConforMix-Boltz

[Rakshitha-Ireddi]

Authors:
Ireddi Rakshitha, Devavarapu Yaswanth,

Overview

This PR adds a fully additive, end-to-end test suite to the ConforMix repository for the Boltz implementation. The goal is to enable reliable, standardized testing of ConforMix-Boltz functionality, without modifying any existing model or sampling code.

All changes are confined to a new conformix_boltz/tests/ module and pytest.ini configuration.

Motivation

ConforMix provides:

• Strong inference-time sampling via Twisted Diffusion Sampling (TDS)
• Two implementations: ConforMix-Boltz (primary) and ConforMix-BioEmu (alternative)
• Comprehensive test coverage for BioEmu implementation

However, the repository currently lacks:

• Test coverage for ConforMix-Boltz (critical gap)
• Automated testing framework for the primary implementation
• Standardized test fixtures and utilities
• Integration test framework for end-to-end validation

This test suite fills that gap by providing a research-focused testing framework suitable for:

• Regression testing
• Code reliability and maintainability
• Continuous integration setup
• Foundation for future test expansion

What's Included

New conformix_boltz/tests/ Module

1. __init__.py - Test package initialization
2. conftest.py - Pytest fixtures and configuration:
   • Temporary directory fixtures
   • Example FASTA file fixtures
   • Example trajectory fixtures
   • CIF file fixtures
3. test_utils.py - Unit tests for utility functions:
   • CIF file discovery and loading
   • Trajectory filtering (physicality checks)
   • Structure combination utilities
   • File processing functions
4. test_run_conformixrmsd.py - Tests for main script:
   • FASTA parsing and validation
   • Argument parsing
   • Sequence length extraction
5. test_integration.py - Integration test framework:
   • End-to-end pipeline tests (marked for manual execution)
   • Data processing pipeline tests
   • Full workflow validation

Configuration

• pytest.ini - Pytest configuration with:
  • Test discovery patterns
  • Custom markers (integration, slow, unit)
  • Output formatting
  • Coverage setup hooks

Key Features

Comprehensive Test Coverage

• Unit Tests: Test individual functions in isolation
• Integration Tests: Test full workflows end-to-end
• Fixtures: Reusable test data and configurations
• Markers: Organized test categories for selective execution

Test Organization

• Fast Unit Tests: Quick validation of core functions
• Integration Tests: Full pipeline tests (require GPU/model, marked appropriately)
• Slow Tests: Long-running validation tests (separately marked)

Developer-Friendly

• Clear test structure following pytest conventions
• Comprehensive fixtures for common test scenarios
• Well-documented test functions
• Easy to extend with additional tests

Usage

Running Tests

# Run all tests
pytest conformix_boltz/tests/ -v

# Run only unit tests (fast)
pytest conformix_boltz/tests/ -v -m "not integration and not slow"

# Run integration tests (requires GPU/model)
pytest conformix_boltz/tests/test_integration.py -v -m integration

# Run with coverage
pytest conformix_boltz/tests/ --cov=boltz --cov-report=html

Test Markers

• @pytest.mark.unit - Fast unit tests
• @pytest.mark.integration - Integration tests requiring model/GPU
• @pytest.mark.slow - Long-running tests

Impact

Immediate Benefits

• Reliability: Catch regressions before they reach production
• Maintainability: Tests serve as documentation and examples
• Confidence: Safe refactoring with test coverage
• CI/CD Ready: Foundation for automated testing

Future Benefits

• Enables continuous integration setup
• Supports test-driven development
• Provides examples for contributors
• Establishes testing patterns for the codebase

Testing Strategy

Current Coverage

• Utility functions (CIF processing, trajectory filtering)
• Main script components (FASTA parsing, argument handling)
• Integration test framework (ready for expansion)

Future Expansion

• Additional unit tests for model components
• More integration tests for different workflows
• Performance benchmarks
• Edge case validation

Compatibility

• Fully Additive: No changes to existing code
• Non-Breaking: All existing functionality preserved
• Optional: Tests can be run independently
• Backward Compatible: Works with existing codebase

Files Changed

conformix_boltz/
├── pytest.ini (new)
└── tests/ (new)
    ├── __init__.py
    ├── conftest.py
    ├── test_utils.py
    ├── test_run_conformixrmsd.py
    └── test_integration.py

Dependencies

No new dependencies required. Uses existing pytest infrastructure (already in project dependencies).

Next Steps

1. Expand test coverage for additional modules
2. Set up CI/CD pipeline with automated testing
3. Add performance benchmarks
4. Integrate with coverage reporting tools

References

• Pytest documentation: https://docs.pytest.org/
• ConforMix paper: arXiv:2512.03312
• Repository: https://github.com/drorlab/conformix