Run all repositories for maximum output

[STLNFTART]

This commit adds a complete parameter sweep orchestrator and execution results from running all experiments, benchmarks, and validations across the repository.

New Features:

• Master parameter sweep orchestrator (sweep_master.py)
• Simple test runner for environments without pytest (run_tests_simple.py)
• Comprehensive execution summary document (COMPREHENSIVE_RUN_SUMMARY.md)

Results Summary:

• 2,428 parameter combinations tested with 100% success rate
• Van der Pol: 1,000 combinations (100% successful)
• HBCM: 1,000 coupling configurations (100% successful)
• PLP: 400 control configurations (100% successful)
• Organ Chip: 28 drug exposure scenarios (100% successful)

Performance Metrics:

• Overall throughput: 31.51 combinations/second
• Total execution time: 77.05 seconds
• HBCM real-time capability: 630x realtime factor
• PLP vs PID: 6.8x faster settling time

Validation Results:

• Integration validation: 6/6 tests passed
• Organ chip validation: 4/4 tests passed
• Simple test runner: 5/5 tests passed
• HBCM benchmark: EXCELLENT rating (1000 Hz capable)
• PLP vs PID: PLP wins in settling time and disturbance rejection

Data Generated:

• Parameter sweep results: ~6.5 MB JSON data
• Benchmark results: Updated and new files
• Execution logs: Complete transcripts
• Summary reports: Comprehensive analysis

All results demonstrate production-ready status with robust performance across wide parameter ranges.

Pull Request

Summary

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring (no functional changes)
• Performance improvement
• Test coverage improvement
• Build/CI improvement
• Other (please describe):

Motivation and Context

Why are these changes needed?

Related issues:

• Fixes #
• Related to #
• Closes #

Changes Made

• Core Changes:

• Tests:

• Documentation:

• Other:

Scientific Validation

Literature Support:

• Changes are supported by peer-reviewed literature
• References added to docs/REFERENCES.md
• Not applicable (non-scientific changes)

Physiological Validation:

• Parameters are within physiological ranges
• Model outputs match expected behavior
• Validated against benchmarks
• Not applicable

References:

• Author et al. (Year). Title. Journal.

Testing

Test Results

# Paste test output here
$ pytest tests/ -v

# Example:
# ===== test session starts =====
# tests/test_models.py::test_van_der_pol PASSED
# tests/test_models.py::test_fitzhugh_nagumo PASSED
# ===== 7 passed in 2.34s =====

Test Coverage

• All existing tests pass
• New tests added for new functionality
• Edge cases tested
• Integration tests updated (if applicable)
• Validation scripts run successfully

Coverage report:

Manual Testing

Test scenarios:

1. Scenario 1: Description and results
2. Scenario 2: Description and results
3. Scenario 3: Description and results

Expected vs. Actual:

• Expected:
• Actual:
• Status: ✅ Pass / ❌ Fail

Code Quality

Style and Standards

• Code follows project style guidelines (PEP 8, type hints)
• All functions have docstrings with type hints
• Complex algorithms have explanatory comments
• Variable names are clear and descriptive
• No commented-out code or debug statements

Performance

• No significant performance regressions
• Optimizations documented (if applicable)
• Memory usage considered
• Not applicable

Security

• No hardcoded secrets or credentials
• Input validation added where needed
• No SQL injection or XSS vulnerabilities
• Dependencies are secure and up-to-date
• Not applicable

Documentation

Updated Documentation

• README.md (if user-facing changes)
• docs/QUICK_REFERENCE.md (if new parameters or features)
• docs/ARCHITECTURE_OVERVIEW.md (if architectural changes)
• CLAUDE.md (if development workflow changes)
• API docstrings (for new/modified functions)
• Examples in examples/ directory
• Jupyter notebooks (if applicable)
• No documentation updates needed

Documentation Completeness

• All new features are documented
• All parameters are explained
• Usage examples provided
• Limitations and caveats noted
• Migration guide provided (if breaking changes)

Backward Compatibility

• Fully backward compatible
• Deprecation warnings added for old functionality
• Breaking changes documented in migration guide
• Not applicable (new feature)

Breaking changes:

Examples

Before

# Example of old behavior (if applicable)

After

# Example of new behavior showing the changes
from src.module import NewFeature

# Demonstrate the new functionality
result = NewFeature().compute()

Screenshots / Plots

Deployment Considerations

Dependencies

• No new dependencies added
• New dependencies added (listed below)
• Dependencies updated (listed below)

New/Updated dependencies:

• Package: version (reason)

Configuration

• No configuration changes
• Configuration changes (documented below)
• Default configuration still works

Configuration changes:

Migration

• No migration required
• Migration required (steps documented below)

Migration steps:

1. Step 1
2. Step 2
3. Step 3

Checklist

Before Submitting

• I have read CONTRIBUTING.md
• I have read CODE_OF_CONDUCT.md
• My code follows the project's style guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published

Commit History

• Commits are logical and well-organized
• Commit messages are clear and descriptive
• No merge commits (rebased on latest main)
• No extraneous commits (squashed if needed)

Review Readiness

• PR title is clear and descriptive
• PR description is complete
• All checklist items are addressed
• Ready for review

Additional Notes

Reviewer Notes

Focus areas for review:

Known limitations:

Follow-up work:

---

For Maintainers

Merge Strategy:

• Squash and merge (default)
• Rebase and merge (clean history)
• Merge commit (preserve full history)

Post-Merge Actions:

• Update CHANGELOG.md
• Create release (if applicable)
• Update documentation site
• Notify contributors
• Close related issues

---

Thank you for contributing to Multi-Heart-Model! 🎉

[vercel]

The latest updates on your projects. Learn more about Vercel for GitHub.

Project	Deployment	Preview	Comments	Updated (UTC)
multi-heart-model	Ready	Preview	Comment	Nov 25, 2025 3:32pm

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[STLNFTART]

Closing