Aider AI Coding Assistant

An AI-powered pair programming tool configured for the heat-tree project - a self-contained widget for phylogenetic and taxonomic tree visualization with categorical and continuous variables.

What This Skill Does

This skill configures Aider to work seamlessly with the heat-tree codebase, using Claude Sonnet 4.5 for main chat interactions and Claude Haiku for faster editor tasks and commit messages. It automatically watches files for AI coding comments, provides read-only access to key documentation, and integrates with git workflows.

Instructions

Initial Setup

1. Ensure you are in the heat-tree repository root directory

2. Verify the `.aider.conf.yml` file exists with the proper configuration

3. Check that `docs/architecture/summary.md` and `package.json` are accessible for context

Model Configuration

Use the following model setup:

Core Workflow

1. **Start Aider Session**

- Launch Aider from the repository root

- The tool will automatically load read-only context from architecture docs and package.json

- File watching is enabled by default for AI coding comments

2. **Making Code Changes**

- Request code modifications through natural language

- Review proposed changes before they are applied

- Auto-commits are DISABLED - you must manually commit changes

- Use `--show-diffs` flag if you want to see diffs before committing

3. **Working with Repository Context**

- Aider automatically generates a repo map for context

- Read-only files provide architectural understanding without allowing edits

- Specify additional files to edit with `/add <file>` command

- Add read-only reference files with `/read <file>` command

4. **Git Integration**

- Changes are staged but not auto-committed (auto-commits: false)

- Review changes with `git diff` before committing

- Aider respects `.gitignore` and uses `.aiderignore` for additional exclusions

- Works only within current git subtree when needed

5. **File Watching**

- File watching is enabled to detect AI coding comments in your code

- Comments like `# AI: refactor this function` will trigger Aider

- Useful for async collaboration and marking TODO items for AI assistance

Best Practices

Key Commands

Configuration Notes

Phylogenetic Visualization Context

This project specializes in:

When requesting changes, consider:

Examples

**Example 1: Refactor a visualization component**

```

/add src/components/TreeVisualizer.js

Please refactor the renderNode function to improve performance for trees with >1000 nodes

```

**Example 2: Add feature with context**

```

/read docs/architecture/summary.md

/add src/utils/dataProcessor.js

Add support for continuous variable color mapping with customizable color scales

```

**Example 3: Fix bug with testing**

```

/add src/components/TreeNode.js

Fix the tooltip positioning bug when hovering over leaf nodes

```

Constraints