Developer guide

Introduction

• Introduction
• Intro
• Fork MolSysMT
  • Clone your fork
  • Work with a conda environment
  • Install it
• Development Environment Setup Guide
  • 🚀 Basic Usage
    • 1. Setup without activation
    • 2. Setup and persist activation
  • 🐍 Choosing Python Version
  • 📂 Flexible Execution Paths
  • ⚙️ Options
  • 📊 Diagnostics
  • ✅ Summary
• Contributing: Development Environment with Devcontainers
  • 📦 How it works
  • 🚀 Usage
  • ✅ Advantages over a simple startup script
  • 🔒 Optional: conda-lock
  • 🧭 Summary

New form

• Adding a new form

Warnings

• MolSysMT Warning System — Developer Guide
  • 1) Why custom warnings?
  • 2) Categories
  • 3) Emitting warnings (two patterns)
    • A. Simple message (most cases)
    • B. Parametrized warning class (centralized formatting)
  • 4) Helpers: warn and warn_once (optional convenience)
  • 5) Choosing stacklevel
  • 6) Filtering and configuration (package & user)
  • 7) Deprecation policy
  • 8) Message style guide
  • 9) Testing warnings (pytest)
    • A. Expect a warning
    • B. No warning expected
    • C. Convert to errors in CI (optional)
  • 10) Migration note (from UserWarning + text prefix)
  • 11) Quick reference (cheat sheet)
• MolSysMT Logging and Warning Redirection — Developer Guide
  • 1) Motivation
  • 2) Implementation overview
  • 3) How developers should emit warnings
  • 4) Logger configuration
  • 5) Testing logging output
  • 6) Good practices
  • 7) Example output

Tests

• Testing
  • Unit Tests
  • Continuous Integration
  • Code Coverage

Documentation

• API
  • Docstrings
  • Doctests
• Web
  • MyST