.github/ - GitHub Integration

GitHub-specific configuration and automation ensuring code quality, collaborative development, and continuous integration. Includes CI/CD workflows, issue templates, and integration features.

Overview

graph TD
    subgraph GitHubIntegration[".github/ - GitHub Integration"]
        WORKFLOWS[workflows/<br/>CI/CD pipelines<br/>Automated testing]
        AGENTS[AGENTS.md<br/>Technical documentation<br/>GitHub integration guide]
        README[README.md<br/>Quick reference<br/>This file]
    end

    subgraph Automation["Automation Features"]
        CI[CI Pipeline<br/>Quality assurance<br/>Multi-version testing]
        QUALITY[Code Quality<br/>Linting & formatting<br/>Ruff integration]
        TESTING[Test Coverage<br/>Automated testing<br/>Coverage reports]
    end

    subgraph Collaboration["Collaboration Features"]
        TEMPLATES[Issue Templates<br/>Structured reporting<br/>Bug reports & features]
        PROTECTION[Branch Protection<br/>Quality gates<br/>Required reviews]
        WORKFLOW[Workflow Automation<br/>Automated checks<br/>Status reporting]
    end

    AGENTS --> WORKFLOWS
    WORKFLOWS --> CI
    CI --> QUALITY
    CI --> TESTING
    AGENTS --> TEMPLATES
    TEMPLATES --> PROTECTION
    PROTECTION --> WORKFLOW

    classDef docs fill:#e3f2fd,stroke:#1565c0,stroke-width:2px
    classDef automation fill:#fff3e0,stroke:#e65100,stroke-width:2px
    classDef collaboration fill:#f3e5f5,stroke:#4a148c,stroke-width:2px

    class AGENTS,README docs
    class CI,QUALITY,TESTING automation
    class TEMPLATES,PROTECTION,WORKFLOW collaboration

Loading

Quick Start

CI/CD Status

# Check workflow status
gh workflow list

# View recent runs
gh run list --workflow=CI

# Check current branch status
gh workflow view CI --ref=main

Local CI Simulation

# Simulate CI environment locally
export CI=true
export GITHUB_ACTIONS=true

# Run linting (matches CI)
uvx ruff check infrastructure/ projects/act_inf_metaanalysis/src/
uvx ruff format --check infrastructure/ projects/act_inf_metaanalysis/src/

# Run tests with coverage (matches CI)
uv run pytest tests/infra_tests/ --cov=infrastructure --cov-fail-under=60
uv run pytest projects/act_inf_metaanalysis/tests/ --cov=projects/act_inf_metaanalysis/src --cov-fail-under=90

Key Features

Continuous Integration

• Automated testing across Python versions (3.10, 3.11, 3.12)
• Code quality checks with Ruff linting and formatting
• Coverage validation (60% infrastructure, 90% project minimum)
• Multi-platform support (Ubuntu latest)

Quality Assurance

• Branch protection with required status checks
• Automated PR validation before merge
• Coverage reporting with codecov integration
• Security scanning (future enhancement)

Collaboration Tools

• Issue templates for structured bug reports
• PR templates for consistent pull requests
• Automated labeling and triage
• Status reporting for all contributions

CI Pipeline

Workflow Triggers

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

Pipeline Jobs

Lint & Type Check (lint)

• Python Version: 3.12
• Scope: infrastructure/ and projects/act_inf_metaanalysis/src/
• Tools: Ruff (linting + formatting), mypy (type checking)
• Duration: ~30 seconds

Infrastructure Tests (test-infra)

• Python Versions: 3.10, 3.11, 3.12 (matrix)
• Scope: tests/infra_tests/ with 60% coverage minimum
• Duration: ~2-3 minutes per version

Project Tests (test-project)

• Python Versions: 3.10, 3.11, 3.12 (matrix)
• Scope: projects/act_inf_metaanalysis/tests/ with 90% coverage minimum
• Duration: ~2-3 minutes per version

Validate Manuscripts (validate)

• Python Version: 3.12
• Scope: Manuscript markdown validation and project import verification
• Depends on: lint

Security Scan (security)

• Python Version: 3.12
• Scope: Dependency audit (pip-audit) and code scan (bandit)
• Depends on: lint

Performance Check (performance)

• Python Version: 3.12
• Scope: Import time benchmarks (must complete under 5 seconds)
• Depends on: test-infra, test-project

Status Checks

# Required status checks for main branch
- lint (Python 3.12)
- test-infra (Python 3.10, 3.11, 3.12)
- test-project (Python 3.10, 3.11, 3.12)
- validate
- security
- performance

Branch Protection

Recommended Setup

# GitHub Branch Protection Rules
required_status_checks:
  - lint
  - test-infra (3.10)
  - test-infra (3.11)
  - test-infra (3.12)
  - test-project (3.10)
  - test-project (3.11)
  - test-project (3.12)
  - validate
  - security
  - performance

required_pull_request_reviews:
  required_approving_review_count: 1

restrictions: null

Quality Gates

• Code must pass linting (Ruff check + format)
• Tests must pass on both Python versions
• Coverage requirements must be met
• PR review required before merge

Issue Templates

Available Templates

• Bug Report: Structured bug reporting with reproduction steps
• Feature Request: Feature proposals with use cases
• Documentation: Documentation improvements and corrections

Template Structure

## Description
Brief description of the issue/feature

## Expected Behavior
What should happen?

## Actual Behavior
What actually happens?

## Steps to Reproduce
1. Step 1
2. Step 2
3. Step 3

## Environment
- OS: [e.g., macOS, Ubuntu]
- Python: [e.g., 3.10, 3.11]
- Browser: [if applicable]

Pull Request Template

Required Sections

• Description: Brief description of changes
• Type of Change: Bug fix, new feature, documentation update, etc.
• Testing: What tests were added/modified
• Checklist: Code standards, documentation updates, etc.

Workflow Management

Common Commands

# List workflows
gh workflow list

# View workflow details
gh workflow view CI

# Run workflow manually (if workflow_dispatch enabled)
gh workflow run CI

# Check workflow status
gh run list --workflow=CI --limit=5

Debugging Failures

# View failed run logs
gh run view <run-id> --log

# Download artifacts
gh run download <run-id>

# Rerun failed jobs
gh run rerun <run-id>

Integration Points

With Repository

• Automatic execution on pushes to main and pull requests
• Status reporting to GitHub UI
• Coverage badges linked to codecov
• Branch protection integration

With Development

• Pre-merge validation ensures code quality
• Automated feedback on pull requests
• Coverage tracking over time
• Multi-version compatibility assurance

Customization

Adding New Workflows

# .github/workflows/new-workflow.yml
name: New Workflow
on:
  push:
    branches: [main]

jobs:
  new-job:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: New step
        run: echo "Custom workflow logic"

Modifying CI Pipeline

1. Edit workflows/ci.yml
2. Test changes locally first
3. Commit and create pull request
4. Monitor CI results
5. Update documentation if needed

Troubleshooting

Common Issues

Workflow Not Triggering

# Check workflow file syntax
gh workflow run --list

# Verify trigger conditions match
# Check branch name, file paths, etc.

Linting Failures

# Fix locally first
uvx ruff check infrastructure/ projects/act_inf_metaanalysis/src/ --fix
uvx ruff format infrastructure/ projects/act_inf_metaanalysis/src/

# Commit fixes
git add .
git commit -m "fix: linting issues"

Test Failures

# Run infrastructure tests locally
uv run pytest tests/infra_tests/ -v

# Run project tests locally
uv run pytest projects/act_inf_metaanalysis/tests/ -v

# Debug specific test
uv run pytest tests/infra_tests/test_specific.py::TestClass::test_method -s

Coverage Issues

# Check infrastructure coverage locally
uv run pytest tests/infra_tests/ --cov=infrastructure --cov-report=html
open htmlcov/index.html

# Check project coverage locally
uv run pytest projects/act_inf_metaanalysis/tests/ --cov=projects/act_inf_metaanalysis/src --cov-report=html
open htmlcov/index.html

Security

Secret Management

• GitHub Secrets: Encrypted storage for tokens
• Environment Variables: Secure value injection
• Access Control: Minimal required permissions
• Audit Logging: Secret access tracking

Security Scanning

# Active in CI security job
- name: Dependency audit
  run: uv run pip-audit
- name: Code security scan
  run: uv run bandit -r infrastructure/ projects/act_inf_metaanalysis/src/

Monitoring

Pipeline Metrics

• Success Rate: Percentage of successful builds
• Build Duration: Average execution time
• Coverage Trends: Test coverage over time
• Failure Patterns: Common failure modes

Integration Monitoring

• Status Checks: Real-time build status
• Coverage Reports: Automated coverage uploads
• Performance Tracking: Build time monitoring
• Quality Metrics: Automated quality assessment

See Also

• AGENTS.md - Complete GitHub integration guide
• workflows/AGENTS.md - CI/CD workflow documentation
• ../docs/development/CONTRIBUTING.md - Contribution guidelines
• ../docs/operational/CI_CD_INTEGRATION.md - CI/CD integration guide