segment with cbs method - threshold #450
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| name: Claude Code | |
| on: | |
| # Interactive: Respond to @claude mentions | |
| issue_comment: | |
| types: [created] | |
| pull_request_review_comment: | |
| types: [created] | |
| pull_request_review: | |
| types: [submitted] | |
| issues: | |
| types: [opened, assigned] | |
| jobs: | |
| claude: | |
| if: | | |
| (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) || | |
| (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) || | |
| (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) || | |
| (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude'))) | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| issues: write | |
| id-token: write | |
| actions: read # Required for Claude to read CI results on PRs | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| - name: Run Claude Code | |
| id: claude | |
| uses: anthropics/claude-code-action@beta | |
| with: | |
| claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} | |
| additional_permissions: | | |
| actions: read | |
| # Custom instructions for CNVkit | |
| custom_instructions: | | |
| This is a bioinformatics Python package for copy number variant detection. | |
| - Follow the project's code style conventions (see CLAUDE.md) | |
| - All code must work with Python 3.11+ | |
| - Security tools (bandit) are configured to allow subprocess calls needed for bioinformatics tools | |
| - R is required for segmentation (DNAcopy package) | |
| - Pre-commit hooks are configured - run before committing | |
| - Use pytest for testing, not unittest | |
| - Respect the existing architecture (see CLAUDE.md for details) |