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Cristian Sifuentes
Cristian Sifuentes

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Trunk-Based Development Applied to Chemistry Simulations

#git #devops #chemistry #trunkbaseddevelopment

Trunk-Based Development Applied to Chemistry Simulations

Trunk-Based Development Applied to Chemistry Simulations

Streamline your Git workflow with atomic precision—just like molecules in motion.

In software projects that model scientific processes, staying agile and accurate is crucial. Let’s explore Trunk-Based Development (TBD) through a chemistry-inspired scenario: building a molecular dynamics simulation engine for modeling atomic behavior in chemical reactions.

This blog adopts an artistic and structured lens to walk through Git best practices using TBD. We'll move like electrons—quick, clean, and in sync with the main trunk.

What is Trunk-Based Development?

Trunk-Based Development is a Git strategy that emphasizes:

  • One shared branch (main or trunk) as the single source of truth.
  • Fast, frequent integrations of short-lived feature branches.
  • Strong reliance on automated CI/CD pipelines to maintain quality.

It’s ideal for fast iterations and scientific experiments where time-to-insight matters.

Project: Chemistry Engine

We are building a chemistry simulator that:

  • Models particle interactions using Lennard-Jones potentials.
  • Supports real-time temperature control and visualization.
  • Runs CI tests for energy conservation.

Branch Visualization 

(main)        *--*--*--*--*--*--* (live, deployable)
                |  |  |  |  |  |
(feature/temp)  *  |  |  |  |  |
                   *  |  |  |  |
                      *  |  |  |
                         *  |  |
                            *--*
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All branches are temporary—no develop, release, or long-lived staging branches.

Git Commands in Practice

1. Start a Feature: Temperature Control 

git checkout main
git pull origin main
git checkout -b feature/temp-control
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2. Write the Feature 

// src/thermostat.ts
export function applyThermostat(particles, targetTemp) {
  // Simple rescaling algorithm
}
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3. Commit Frequently 

git add src/thermostat.ts
git commit -m "feat: implement velocity rescaling thermostat"
git push -u origin feature/temp-control
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4. Merge into Main 

git checkout main
git pull origin main
git merge feature/temp-control
git push origin main
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CI runs:

npm run test
npm run validate-energy-conservation
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Continuous Chemistry with CI/CD

Add a GitHub workflow or GitLab CI config:

on:
  push:
    branches: [main]
jobs:
  simulate:
    steps:
      - run: npm test
      - run: node validate-energy.js
  deploy:
    steps:
      - run: ./deploy-sim-env.sh
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Use Feature Flags for Experimental Code 

if (flags.useThermostat) {
  applyThermostat(particles, 300);
}
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This keeps main deployable even when simulations are incomplete.

Rebase Often 

git checkout feature/temp-control
git pull --rebase origin main
git push --force-with-lease
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Practical Example: Adding Molecule Viewer 

git checkout main
git checkout -b feature/molecule-visualizer
# Write code...
git add .
git commit -m "feat: 3D molecule visualization"
git push -u origin feature/molecule-visualizer
# Merge it!
git checkout main
git merge feature/molecule-visualizer
git push origin main
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Clean Code History

Use interactive rebase to squash noisy commits:

git rebase -i HEAD~5
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Use atomic, clear commit messages:

feat: add force calculation for Lennard-Jones interaction
fix: correct sign in acceleration integration
test: validate total energy conservation
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Combined Git Tricks

Command Purpose
git pull --rebase origin main Sync feature branch
git stash && git stash pop Manage quick switches
git mergetool Resolve visual conflicts
git cherry-pick <hash> Apply hot patches

Key Takeaways

Principle Why It Works
Frequent commits Lower risk of conflicts
Always deployable main Safe for production
Feature flags Allow partial releases
CI/CD enforcement Maintain quality automatically
Short-lived branches Encourage small, reviewable changes

Final Thoughts

Trunk-Based Development in scientific software development is like controlling a lab experiment—clean, controlled, and reactive. With short cycles and continuous delivery, your simulation engine evolves organically—one molecule (commit) at a time.

Harness Git’s precision. Embrace flow. And bring elegance to your code—chemically and structurally.

Follow for more workflow artistry and Git wizardry! ⚛️🚀

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