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Scaffold: add AI GitHub integrations (Copier) and LinkML docs site #1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| name: "Claude Code Action" | ||
| description: "Run Claude Code in GitHub Actions workflows" | ||
|
|
||
| inputs: | ||
| github_token: | ||
| description: "GitHub token with repo and issues permissions" | ||
| required: true | ||
| anthropic_api_key: | ||
| description: "Anthropic API key" | ||
| required: true | ||
| cborg_api_key: | ||
| description: "CBORG API key" | ||
| required: true | ||
| prompt: | ||
| description: "The prompt to send to Claude Code" | ||
| required: false | ||
| default: "" | ||
| prompt_file: | ||
| description: "Path to a file containing the prompt to send to Claude Code" | ||
| required: false | ||
| default: "" | ||
| allowed_tools: | ||
| description: "Comma-separated list of allowed tools for Claude Code to use" | ||
| required: false | ||
| default: "" | ||
| output_file: | ||
| description: "File to save Claude Code output to (optional)" | ||
| required: false | ||
| default: "" | ||
| timeout_minutes: | ||
| description: "Timeout in minutes for Claude Code execution" | ||
| required: false | ||
| default: "10" | ||
| install_github_mcp: | ||
| description: "Whether to install the GitHub MCP server" | ||
| required: false | ||
| default: "false" | ||
| install_artl_mcp: | ||
| description: "Whether to install the ARTL MCP server" | ||
| required: false | ||
| default: "false" | ||
|
|
||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Install uvx | ||
| shell: bash | ||
| run: | | ||
| curl -LsSf https://astral.sh/uv/install.sh | sh | ||
| source $HOME/.cargo/env | ||
| which uvx || echo "uvx not found in PATH, installing via pip" | ||
| pip install uv || true | ||
|
|
||
| - name: Install Claude Code | ||
| shell: bash | ||
| run: npm install -g @anthropic-ai/claude-code | ||
|
|
||
| - name: Install GitHub MCP Server | ||
| if: inputs.install_github_mcp == 'true' | ||
| shell: bash | ||
| run: | | ||
| claude mcp add-json github '{ | ||
| "command": "docker", | ||
| "args": [ | ||
| "run", | ||
| "-i", | ||
| "--rm", | ||
| "-e", | ||
| "GITHUB_PERSONAL_ACCESS_TOKEN", | ||
| "ghcr.io/github/github-mcp-server:sha-ff3036d" | ||
| ], | ||
| "env": { | ||
| "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ inputs.GITHUB_TOKEN }}" | ||
| } | ||
| }' | ||
|
|
||
| - name: Install ARTL MCP Server | ||
| if: inputs.install_artl_mcp == 'true' | ||
| shell: bash | ||
| run: | | ||
| claude mcp add-json artl '{ | ||
| "command": "uvx", | ||
| "args": [ | ||
| "artl-mcp" | ||
| ] | ||
| }' | ||
|
|
||
| - name: Prepare Prompt File | ||
| shell: bash | ||
| id: prepare_prompt | ||
| run: | | ||
| # Check if either prompt or prompt_file is provided | ||
| if [ -z "${{ inputs.prompt }}" ] && [ -z "${{ inputs.prompt_file }}" ]; then | ||
| echo "::error::Neither 'prompt' nor 'prompt_file' was provided. At least one is required." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # Determine which prompt source to use | ||
| if [ ! -z "${{ inputs.prompt_file }}" ]; then | ||
| # Check if the prompt file exists | ||
| if [ ! -f "${{ inputs.prompt_file }}" ]; then | ||
| echo "::error::Prompt file '${{ inputs.prompt_file }}' does not exist." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # Use the provided prompt file | ||
| PROMPT_PATH="${{ inputs.prompt_file }}" | ||
| else | ||
| mkdir -p /tmp/claude-action | ||
| PROMPT_PATH="/tmp/claude-action/prompt.txt" | ||
| echo "${{ inputs.prompt }}" > "$PROMPT_PATH" | ||
| fi | ||
|
|
||
| # Verify the prompt file is not empty | ||
| if [ ! -s "$PROMPT_PATH" ]; then | ||
| echo "::error::Prompt is empty. Please provide a non-empty prompt." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # Save the prompt path for the next step | ||
| echo "PROMPT_PATH=$PROMPT_PATH" >> $GITHUB_ENV | ||
|
|
||
| - name: Run Claude Code | ||
| shell: bash | ||
| id: run_claude | ||
| run: | | ||
| ALLOWED_TOOLS_ARG="" | ||
| if [ ! -z "${{ inputs.allowed_tools }}" ]; then | ||
| ALLOWED_TOOLS_ARG="--allowedTools ${{ inputs.allowed_tools }}" | ||
| fi | ||
|
|
||
| # Set a timeout to ensure the command doesn't run indefinitely | ||
| timeout_seconds=$((${{ inputs.timeout_minutes }} * 60)) | ||
|
|
||
| if [ -z "${{ inputs.output_file }}" ]; then | ||
| # Run Claude Code and output to console | ||
| timeout $timeout_seconds claude \ | ||
| -p \ | ||
| --verbose \ | ||
| --output-format stream-json \ | ||
| "$(cat ${{ env.PROMPT_PATH }})" \ | ||
| ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }} | ||
| else | ||
| # Run Claude Code and tee output to console and file | ||
| timeout $timeout_seconds claude \ | ||
| -p \ | ||
| --verbose \ | ||
| --output-format stream-json \ | ||
| "$(cat ${{ env.PROMPT_PATH }})" \ | ||
| ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }} | tee output.txt | ||
|
|
||
| # Process output.txt into JSON in a separate step | ||
| jq -s '.' output.txt > output.json | ||
|
|
||
| # Extract the result from the last item in the array (system message) | ||
| jq -r '.[-1].result' output.json > "${{ inputs.output_file }}" | ||
|
|
||
| echo "Complete output saved to output.json, final response saved to ${{ inputs.output_file }}" | ||
| fi | ||
|
|
||
| env: | ||
| ANTHROPIC_API_KEY: "." | ||
| ANTHROPIC_AUTH_TOKEN: ${{ inputs.cborg_api_key }} | ||
| GITHUB_TOKEN: ${{ inputs.github_token }} | ||
| ANTHROPIC_BASE_URL: "https://api.cborg.lbl.gov" | ||
| DISABLE_NON_ESSENTIAL_MODEL_CALLS: "1" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| name: "Claude Issue summarize Action" | ||
| description: "Automatically Summarize GitHub issues using Claude Code" | ||
|
|
||
| inputs: | ||
| timeout_minutes: | ||
| description: "Timeout in minutes for execution" | ||
| required: false | ||
| default: "5" | ||
| anthropic_api_key: | ||
| description: "Anthropic API key" | ||
| required: true | ||
| cborg_api_key: | ||
| description: "CBORG API key" | ||
| required: true | ||
| github_token: | ||
| description: "GitHub token with repo and issues permissions" | ||
| required: true | ||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Checkout repository code | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Create prompt file | ||
| shell: bash | ||
| run: | | ||
| mkdir -p /tmp/claude-prompts | ||
| cat > /tmp/claude-prompts/claude-issue-summarize-prompt.txt << 'EOF' | ||
| You're an Summarization assistant for GitHub issues. Your task is to analyze the issue, look up related issues, and summarize the issue. | ||
|
|
||
| Remember that this repo is primarily a note-taking and memory device for Chris Mungall, so anything you can do to enhance and enrich that would be helpful. | ||
|
|
||
| IMPORTANT: Don't make any PRs. You should ONLY post a response, IN THE SAME ISSUE. | ||
|
|
||
| Issue Information: | ||
| - REPO: ${{ github.repository }} | ||
| - ISSUE_NUMBER: ${{ github.event.issue.number }} | ||
|
|
||
| TASK OVERVIEW: | ||
|
|
||
| 1. First, use your judgement to determine the course of action. | ||
| - If the issue is an epic or has links to other issues, read those issues, and summarize them. Summarize their status etc. Given an overall summary. | ||
| - If the issue is an idea or a vague high level description, run with the idea, do deep research, give heloful suggestions with links to relevant papers etc. | ||
| - If there are links in the issue to websites, database entities, etc, then look these up. | ||
| - If there are links or references to papers, then looks these up and summarize (don't guess content - if you can't access the paper, then say "I can't access the paper") | ||
| - Try using artl-mcp to get paper fulltext. | ||
| - If you want a more powerful AI agent to take on this one and make a PR, use this magic phrase: `@dragon-ai-agent please <INSTRUCTIONS>` | ||
|
|
||
| 2. Next, use the GitHub tools to get context about the issue: | ||
| - You have access to these github tools: | ||
| - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels | ||
| - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments | ||
| - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting) | ||
| - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues | ||
| - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled | ||
| - You can also use web searching and fetching. | ||
|
|
||
| - It's okay to not add any information if the issue is not clear. | ||
| EOF | ||
|
|
||
| - name: Run Claude Code | ||
| uses: ./.github/actions/claude-code-action | ||
| with: | ||
| prompt_file: /tmp/claude-prompts/claude-issue-summarize-prompt.txt | ||
| allowed_tools: "Bash(gh label list),WebFetch,Fetch,LS,mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__add_issue_comment,mcp__github__search_issues,mcp__github__list_issues" | ||
| install_github_mcp: "true" | ||
| install_artl_mcp: "true" | ||
| timeout_minutes: ${{ inputs.timeout_minutes }} | ||
| anthropic_api_key: ${{ inputs.anthropic_api_key }} | ||
| cborg_api_key: ${{ inputs.cborg_api_key }} | ||
| github_token: ${{ inputs.github_token }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| name: "Claude Issue Triage Action" | ||
| description: "Automatically triage GitHub issues using Claude Code" | ||
|
|
||
| inputs: | ||
| timeout_minutes: | ||
| description: "Timeout in minutes for execution" | ||
| required: false | ||
| default: "5" | ||
| anthropic_api_key: | ||
| description: "Anthropic API key" | ||
| required: true | ||
| cborg_api_key: | ||
| description: "CBORG API key" | ||
| required: true | ||
| github_token: | ||
| description: "GitHub token with repo and issues permissions" | ||
| required: true | ||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Checkout repository code | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Create prompt file | ||
| shell: bash | ||
| run: | | ||
| mkdir -p /tmp/claude-prompts | ||
| cat > /tmp/claude-prompts/claude-issue-triage-prompt.txt << 'EOF' | ||
| You're an issue triage assistant for GitHub issues. Your task is to analyze the issue and select appropriate labels from the provided list. | ||
|
|
||
| IMPORTANT: Don't post any comments or messages to the issue. Your only action should be to apply labels. | ||
|
|
||
| Issue Information: | ||
| - REPO: ${{ github.repository }} | ||
| - ISSUE_NUMBER: ${{ github.event.issue.number }} | ||
|
|
||
| TASK OVERVIEW: | ||
|
|
||
| 1. First, fetch the list of labels available in this repository by running: `gh label list`. Run exactly this command with nothing else. | ||
|
|
||
| 2. Next, use the GitHub tools to get context about the issue: | ||
| - You have access to these tools: | ||
| - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels | ||
| - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments | ||
| - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting) | ||
| - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues | ||
| - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled | ||
| - Start by using mcp__github__get_issue to get the issue details | ||
|
|
||
| 3. Analyze the issue content, considering: | ||
| - The issue title and description | ||
| - The type of issue (bug report, feature request, question, etc.) | ||
| - Technical areas mentioned | ||
| - Severity or priority indicators | ||
| - User impact | ||
| - Components affected | ||
|
|
||
| 4. Select appropriate labels from the available labels list provided above: | ||
| - Choose labels that accurately reflect the issue's nature | ||
| - Be specific but comprehensive | ||
| - Select priority labels if you can determine urgency (high-priority, med-priority, or low-priority) | ||
| - Consider platform labels (android, ios) if applicable | ||
| - If you find similar issues using mcp__github__search_issues, consider using a "duplicate" label if appropriate. Only do so if the issue is a duplicate of another OPEN issue. | ||
|
|
||
| 5. Apply the selected labels: | ||
| - Use mcp__github__update_issue to apply your selected labels | ||
| - DO NOT post any comments explaining your decision | ||
| - DO NOT communicate directly with users | ||
| - If no labels are clearly applicable, do not apply any labels | ||
|
|
||
| IMPORTANT GUIDELINES: | ||
| - Be thorough in your analysis | ||
| - Only select labels from the provided list above | ||
| - DO NOT post any comments to the issue | ||
| - Your ONLY action should be to apply labels using mcp__github__update_issue | ||
| - It's okay to not add any labels if none are clearly applicable | ||
| EOF | ||
|
|
||
| - name: Run Claude Code | ||
| uses: ./.github/actions/claude-code-action | ||
| with: | ||
| prompt_file: /tmp/claude-prompts/claude-issue-triage-prompt.txt | ||
| allowed_tools: "Bash(gh label list),mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__search_issues,mcp__github__list_issues" | ||
| install_github_mcp: "true" | ||
| timeout_minutes: ${{ inputs.timeout_minutes }} | ||
| anthropic_api_key: ${{ inputs.anthropic_api_key }} | ||
| cborg_api_key: ${{ inputs.cborg_api_key }} | ||
| github_token: ${{ inputs.github_token }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ["realmarcin"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ../AGENTS.md |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| name: "Copilot Setup Steps" | ||
|
|
||
|
|
||
| # Automatically run the setup steps when they are changed to allow for easy validation, and | ||
| # allow manual testing through the repository's "Actions" tab | ||
| on: | ||
| workflow_dispatch: | ||
| push: | ||
| paths: | ||
| - .github/workflows/copilot-setup-steps.yml | ||
| pull_request: | ||
| paths: | ||
| - .github/workflows/copilot-setup-steps.yml | ||
|
|
||
| jobs: | ||
| # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot. | ||
| copilot-setup-steps: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| # Set the permissions to the lowest permissions possible needed for your steps. | ||
| # Copilot will be given its own token for its operations. | ||
| permissions: | ||
| # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete. | ||
| contents: read | ||
|
|
||
| # You can define any steps you want, and they will run before the agent starts. | ||
| # If you do not check out your code, Copilot will do this for you. | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Install uv | ||
| uses: astral-sh/setup-uv@v5 | ||
|
|
||
| - name: Install Python tools | ||
| run: | | ||
| uv sync | ||
| source .venv/bin/activate | ||
| shell: bash | ||
|
|
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The ANTHROPIC_API_KEY is set to a literal dot (".") which is likely incorrect. This should either use the anthropic_api_key input or be removed if CBORG authentication is the intended method.