ci: add reusable phenotype workflows

[KooshaPari]

This PR adds standardized CI workflows from the phenotype-infrakit reusable workflow library.

Workflows Added

• CI workflow (quality-gate.yml)
• Coverage workflow (coverage.yml)
• Publishing workflow (publish-*.yml)

Benefits

• Consistent quality gates across phenotype ecosystem
• Automated publishing to registries
• Standardized CI/CD

Testing

• Workflows use the centralized phenotype-infrakit/.github/workflows/ definitions

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 18c94868-e12b-44b4-9886-b596ba54c36a

📥 Commits

Reviewing files that changed from the base of the PR and between 80e7b8d and 046dd49.

📒 Files selected for processing (2)

• .github/workflows/ci.yml
• .github/workflows/coverage.yml

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch chore/add-reusable-workflows

✨ Simplify code

• Create PR with simplified code
• Commit simplified code in branch chore/add-reusable-workflows

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[kilo-code-bot]

Code Review Summary

Status: 1 Issue Found | Recommendation: Request Changes

Overview

Severity	Count
CRITICAL	1
WARNING	0
SUGGESTION	0

Issue Details (click to expand)

CRITICAL

File	Line	Issue
.github/workflows/ci.yml	12	Workflow file extension mismatch - references ci.yaml while coverage.yml references coverage.yml. This inconsistency could cause the CI workflow to fail to load or 404 if the reusable workflow file doesn't exist with the .yaml extension.

Files Reviewed (2 files)

• .github/workflows/ci.yml - 1 issue
• .github/workflows/coverage.yml - 0 issues

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Analysis:

The PR correctly adds two reusable CI workflows from the KooshaPari/phenotype-infrakit repo. Both workflows:

• Trigger on push and PR to main/master branches
• Use secrets: inherit to pass secrets to reusable workflows
• Follow the expected workflow structure

However, there's an inconsistency: ci.yml references ci.yaml (line 12) while coverage.yml references coverage.yml (line 12). This should be aligned - both should use either .yml or .yaml consistently.

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