Analyze rapid DNA sequencing

[ruvnet]

This pull request introduces a comprehensive CI/CD pipeline for the genomic-vector-analysis package, adding robust automation, quality gates, security scanning, and extensive documentation. It creates and updates multiple GitHub Actions workflows, adds configuration files for code quality and dependency management, and provides detailed guides and overviews for maintainers. The setup is designed for high code quality, security, and ease of maintenance.

CI/CD Pipeline and Workflow Automation

• Added five GitHub Actions workflows (test.yml, build.yml, publish.yml, docs.yml, quality.yml) to automate testing, building, publishing, documentation, and quality checks, with clearly defined triggers and quality gates such as code coverage, performance, and security scanning. (.github/CI_CD_SETUP_SUMMARY.md, .github/CI_CD_SETUP_SUMMARY.mdR1-R342)
• Updated and documented workflow dependencies, matrix strategies, and performance/security optimizations, including caching and parallel execution for efficient CI runs. (.github/WORKFLOWS_OVERVIEW.md, .github/WORKFLOWS_OVERVIEW.mdR1-R194)

Configuration and Quality Enforcement

• Introduced configuration files for code formatting (.prettierrc), linting (.eslintrc.json), Node version management (.nvmrc), and markdown link checking (markdown-link-check-config.json), ensuring consistency and codebase health. (.github/FILES_CREATED.md, [1]; .github/markdown-link-check-config.json, [2]
• Added and configured dependabot.yml to automate dependency updates for npm, Cargo, and GitHub Actions, with reviewer assignments and update strategies. (.github/dependabot.yml, .github/dependabot.ymlR1-R59)

Documentation and Onboarding

• Created extensive documentation, including a setup summary, workflow overview, CI/CD guide, and a complete file manifest to aid onboarding, troubleshooting, and future enhancements. (.github/CI_CD_SETUP_SUMMARY.md, [1]; .github/WORKFLOWS_OVERVIEW.md, [2]; .github/FILES_CREATED.md, [3]

Security and Release Management

• Integrated multi-layer security scanning (npm audit, Snyk, CodeQL, dependency review) and provenance attestation for NPM releases, with instructions for setting up required GitHub secrets. (.github/CI_CD_SETUP_SUMMARY.md, .github/CI_CD_SETUP_SUMMARY.mdR1-R342)

Next Steps and Recommendations

• Provided actionable next steps, including secrets setup, GitHub Pages enablement, branch protection, and suggestions for future improvements like end-to-end tests and canary deployments. (.github/CI_CD_SETUP_SUMMARY.md, .github/CI_CD_SETUP_SUMMARY.mdR1-R342)

References:
[1] [2] [3] [4] [5]

[github-advanced-security]

This pull request sets up GitHub code scanning for this repository. Once the scans have completed and the checks have passed, the analysis results for this pull request branch will appear on this overview. Once you merge this pull request, the 'Security' tab will show more code scanning analysis results (for example, for the default branch). Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results. For more information about GitHub code scanning, check out the documentation.

To fix this problem, simply remove the declaration of the unused variable db from the function. This means deleting line 17 (const db = new GenomicVectorDB();). There is no need to remove the import of GenomicVectorDB at the top, since you are only to address code you've been shown and not assume the state of other files or usages. All changes are within the file packages/cli/src/commands/export.ts.

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To fix the issue, remove the variable assignment const db = ... and replace it with simply constructing the GenomicVectorDB instance. If the side effect of the constructor is required (the database is created/initialized upon instantiation), we should keep the instantiation, but eliminate the unused variable db. This is done by simply calling new GenomicVectorDB(...) without assignment. The fix should be confined to line 17.

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The best way to fix this problem is to remove the unused import of inquirer from the file packages/cli/src/commands/interactive.ts. This reduces clutter and avoids possible confusion about which modules are actually in use. We should simply delete line 2: import inquirer from 'inquirer';. All other code remains unchanged, and there are no additional dependencies or logic required.

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The correct way to address this problem is to remove the unused assignment to the threshold variable on line 19. This involves deleting the line:

const threshold = options.threshold ? parseFloat(options.threshold) : undefined;

from the searchCommand function in packages/cli/src/commands/search.ts. No further changes are necessary, as there are no other references to threshold in the snippet provided.

To fix the unused variable error, remove the line where filters is assigned, as the value is parsed but never used later in the code. The relevant line is:

20:     const filters = options.filters ? JSON.parse(options.filters) : undefined;

This line can be deleted without affecting any existing functionality, as no other references to filters are present within the function.

No additional imports, methods, or definitions are required.

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To fix this issue, simply remove the line that declares and initializes db (line 14: const db = new GenomicVectorDB();). There is no need to adjust other lines or replace usages, as db is not referenced elsewhere. The initialization itself does not affect any other part of the code, so its removal will not alter current behavior.

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