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Agent Instructions

Workflow

  • Work on dev branch
  • Make atomic commits
  • Do not merge to main unless the user explicitly asks for it
  • When a change is merged to main, determine the next version bump automatically from the code changes, create the new tag automatically, and push all resulting commits and tags

Commit Message Format

Follow conventional commit format. First line must be less than 78 characters.

Format

<type>(<scope>): <icon> <short description>

Types

  • feat: ✨ A new feature
  • fix: 🐛 A bug fix
  • docs: 📝 Documentation updates
  • style: 💄 Formatting, missing semi-colons
  • refactor: ♻️ Code change that neither fixes a bug nor adds a feature
  • test: ✅ Adding or correcting tests
  • chore: 🔧 Build process or auxiliary tools
  • ci: 👷 CI configuration files and scripts
  • build: 🏗️ Build system changes
  • revert: ⏪ Reverting changes
  • wip: 🚧 Work in progress

Rules

  • Long description should explain why the change was made
  • Reference related issues (e.g., Fixes #123)
  • If breaking change, include BREAKING CHANGE: <description>

Python Coding Conventions (applyTo: **/*.py)

General

  • Write clear and concise comments for each function
  • Use descriptive names with type hints
  • Break down complex functions into smaller ones
  • Prioritize readability and clarity

Documentation

  • Use numpy-style docstrings (PEP 257)

  • Include docstrings immediately after def or class

  • Docstring format:

    def function(param: type) -> return_type:
    """Short summary.

    Longer description if needed.

    Parameters:
        param (type): Description

    Returns:
        return_type: Description
    """

Style

  • Follow PEP 8 style guide
  • Use 4 spaces for indentation
  • Max line length: 79 characters
  • Group imports: stdlib, third-party, local (separated by blank lines)

Testing

  • Include test cases for critical paths
  • Account for edge cases (empty inputs, invalid types)
  • For ImageJ/Fiji code, add "Works on" section (2D, 3D, 4D, etc.)

README Structure (for new projects)

  1. Logo: Generate a project-specific logo
  2. Title: Project name as # header
  3. Purpose: 1-2 paragraph explanation
  4. Requirements: Dependencies, hardware, environment
  5. Input and Expected Output: Data formats, visualization types
  6. Detailed Explanation: Architecture, logic, inner workings

Markdown Conventions (applyTo: **/*.md)

Follow all markdownlint (MDxxx) rules:

  • Use ATX-style headers (#, ##, etc.)
  • Include a blank line after headers
  • Use fenced code blocks with language identifiers
  • Keep lines under 80 characters
  • Use consistent indentation (2 or 4 spaces)
  • No trailing whitespace
  • Include alt text for images
  • Use inline links, keep URLs on separate lines if long
  • Use ordered lists for sequential steps, unordered for non-sequential
  • Use consistent quote styles (double quotes)
  • Include proper spacing between block elements