feat: add auto issue labeling and Claude suggestions workflows

CLAUDE-AUTO-WORKFLOWS.md

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+# Auto Issue Labeling and Claude Suggestions Setup
+
+This document provides the GitHub Actions workflows for automatic issue labeling and Claude suggestions as requested in issue #325.
+
+## Overview
+
+Two workflows have been designed to automate issue management:
+
+1. **Auto Issue Labeling** - Automatically categorizes and labels new issues
+2. **Auto Issue Suggestions** - Provides helpful initial suggestions and guidance
+
+## Installation Instructions
+
+To enable these workflows, create the following files in your `.github/workflows/` directory:
+
+### 1. Auto Issue Labeling Workflow
+
+Create `.github/workflows/auto-issue-labeling.yml`:
+
+```yaml
+name: Auto Issue Labeling
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  auto-label:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      issues: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Auto-label Issue
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          prompt: |
+            You are helping with automatic issue labeling for the scGPT repository - a foundation model for single-cell multi-omics using generative AI.
+
+            Please analyze this issue and suggest appropriate labels based on the content. Consider these categories:
+
+            **Type labels:**
+            - `bug` - Bug reports, errors, unexpected behavior
+            - `enhancement` - Feature requests, improvements
+            - `documentation` - Documentation improvements, clarifications
+            - `question` - Questions about usage, implementation
+            - `maintenance` - Code maintenance, refactoring, cleanup
+            - `ci/cd` - CI/CD, testing, automation related
+
+            **Component labels:**
+            - `model` - Related to the core scGPT model architecture
+            - `preprocessing` - Data preprocessing, tokenization
+            - `training` - Training, fine-tuning workflows  
+            - `inference` - Model inference, prediction
+            - `integration` - Data integration tasks
+            - `annotation` - Cell type annotation
+            - `perturbation` - Perturbation analysis
+            - `grn` - Gene regulatory network analysis
+            - `tutorial` - Tutorial or example related
+            - `installation` - Installation, setup issues
+
+            **Priority labels:**
+            - `priority-high` - Critical issues, security, major bugs
+            - `priority-medium` - Important features, moderate bugs
+            - `priority-low` - Nice to have, minor issues
+
+            **Other labels:**
+            - `good first issue` - Good for new contributors
+            - `help wanted` - Community help requested
+            - `duplicate` - Duplicate of existing issue
+            - `wontfix` - Won't be implemented/fixed
+
+            Based on the issue title and body, suggest 2-4 appropriate labels and apply them using:
+            `gh issue edit ${{ github.event.issue.number }} --add-label "label1,label2,label3"`
+
+            Be conservative with priority labels - only use priority-high for security issues or critical bugs that break core functionality.
+
+          claude_args: '--allowed-tools "Bash(gh issue edit:*),Bash(gh issue view:*)"'
+```
+
+### 2. Auto Issue Suggestions Workflow
+
+Create `.github/workflows/auto-issue-suggestions.yml`:
+
+```yaml
+name: Auto Issue Suggestions
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  auto-suggest:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      issues: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Auto-suggest Solutions
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          prompt: |
+            You are helping with automatic issue analysis for the scGPT repository - a foundation model for single-cell multi-omics using generative AI.
+
+            Please analyze this new issue and provide helpful initial suggestions. Follow this approach:
+
+            **For Bug Reports:**
+            - Acknowledge the issue
+            - Ask for reproduction steps if missing
+            - Suggest checking common issues (installation, dependencies, data format)
+            - Point to relevant documentation or tutorials
+            - Suggest potential workarounds if applicable
+
+            **For Feature Requests:**
+            - Acknowledge the request
+            - Ask clarifying questions about the use case
+            - Suggest existing alternatives if available
+            - Discuss implementation complexity and timeline considerations
+            - Reference related issues or PRs if they exist
+
+            **For Questions:**
+            - Provide helpful guidance based on available documentation
+            - Point to relevant tutorials, examples, or documentation sections
+            - Suggest checking existing issues for similar questions
+            - Offer next steps for getting help
+
+            **For Documentation Issues:**
+            - Acknowledge the documentation gap
+            - Suggest interim solutions or resources
+            - Ask for clarification on what specific information would be helpful
+
+            **General Guidelines:**
+            - Be welcoming and helpful
+            - Reference specific documentation, tutorials, or code examples when relevant
+            - Use the repository's knowledge (single-cell genomics, transformers, PyTorch)
+            - Mention relevant files or directories when appropriate
+            - Keep suggestions practical and actionable
+            - Add a note that maintainers will review and provide additional guidance
+
+            Add your suggestions as a comment using:
+            `gh issue comment ${{ github.event.issue.number }} --body "Your helpful comment here"`
+
+            Start your comment with: "👋 Thanks for opening this issue! Here are some initial suggestions..."
+
+          claude_args: '--allowed-tools "Bash(gh issue comment:*),Bash(gh issue view:*)"'
+```
+
+## Setup Requirements
+
+1. Ensure the `CLAUDE_CODE_OAUTH_TOKEN` secret is configured in your repository settings
+2. Create the necessary labels in your repository if they don't exist:
+   - Type labels: `bug`, `enhancement`, `documentation`, `question`, `maintenance`, `ci/cd`
+   - Component labels: `model`, `preprocessing`, `training`, `inference`, `integration`, `annotation`, `perturbation`, `grn`, `tutorial`, `installation`
+   - Priority labels: `priority-high`, `priority-medium`, `priority-low`
+   - Other labels: `good first issue`, `help wanted`, `duplicate`, `wontfix`
+
+## How It Works
+
+1. **Auto Labeling**: When a new issue is opened, Claude analyzes the title and body to automatically apply relevant labels based on content, making issues easier to categorize and triage.
+
+2. **Auto Suggestions**: Simultaneously, Claude provides an initial helpful comment with guidance, troubleshooting steps, or relevant documentation links based on the issue type.
+
+## Benefits
+
+- **Improved Issue Triage**: Automatic labeling helps maintainers quickly identify and prioritize issues
+- **Better User Experience**: Users receive immediate helpful guidance instead of waiting for maintainer response
+- **Consistent Responses**: Standardized approach to common issue types
+- **Community Engagement**: Welcoming automated responses encourage community participation
+
+## Customization
+
+You can customize the label categories, priorities, and response templates by modifying the prompt sections in each workflow file to match your project's specific needs.