Add CODEOWNERS file for code review requirements #10

Workflow file for this run

	name: CI/CD Pipeline
Check failure on line 1 in .github/workflows/ci.yml View workflow run for this annotation GitHub Actions / .github/workflows/ci.yml Invalid workflow file `(Line: 14, Col: 11): Unrecognized named-value: 'env'. Located at position 1 within expression: env.PYTHON_DEFAULT_VERSION`

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

	env:
	PYTHON_DEFAULT_VERSION: "3.11"

	jobs:
	test:
	name: Test Python ${{ env.PYTHON_DEFAULT_VERSION }}
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python ${{ env.PYTHON_DEFAULT_VERSION }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PYTHON_DEFAULT_VERSION }}
	cache: 'pip'

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y gcc g++ curl git

	- name: Upgrade pip, setuptools, and wheel
	run: \|
	python -m pip install --upgrade pip setuptools wheel build

	- name: Install PyTorch CPU (for faster CI)
	run: \|
	pip install --no-cache-dir --default-timeout=600 \
	--extra-index-url https://download.pytorch.org/whl/cpu \
	torch==2.1.0+cpu \
	torchvision==0.16.0+cpu \
	torchaudio==2.1.0+cpu

	- name: Install project dependencies
	run: \|
	# Install package in editable mode first
	pip install --no-cache-dir -e ".[dev]"
	# Install remaining dependencies that aren't in dev extras
	pip install --no-cache-dir \
	transformers>=4.34.0 \
	scikit-learn>=1.3.0 \
	pandas>=2.1.1 \
	numpy>=1.26.0 \
	biopython>=1.81 \
	sentencepiece>=0.1.99 \
	accelerate>=0.24.0 \
	datasets>=2.14.0 \
	google-generativeai>=0.7.2 \
	tiktoken>=0.5.0 \
	litellm>=1.50.0 \
	requests>=2.31.0 \
	beautifulsoup4>=4.12.2 \
	lxml>=4.9.0 \
	openpyxl>=3.1.0 \
	xlrd>=2.0.1 \
	tqdm>=4.65.0 \
	python-dotenv>=1.0.0 \
	psutil>=5.9.0 \
	fastapi>=0.104.0 \
	"uvicorn[standard]>=0.23.2" \
	aiohttp>=3.8.6 \
	websockets>=11.0.3 \
	python-multipart>=0.0.5 \
	aiofiles>=0.7.0 \
	pydantic>=2.4.2 \
	typing-extensions>=3.10.0.2 \
	starlette>=0.31.1 \
	click>=8.0.1 \
	h11>=0.12.0 \
	httptools>=0.3.0 \
	PyYAML>=5.4.1 \
	"watchfiles[watchdog]>=1.0.0" \
	wsproto>=1.0.0 \
	tokenizers>=0.14.1 \
	pytz>=2023.3 \
	qdrant-client>=1.7.0

	- name: Install paper-qa from GitHub
	run: \|
	# For Python 3.11, install latest paper-qa from GitHub (supports >=5.0.0)
	echo "Installing paper-qa from GitHub for Python 3.11"
	pip install --no-cache-dir git+https://github.com/Future-House/paper-qa.git \|\| \
	pip install --no-cache-dir "paper-qa>=4.9.0,<5.0.0"

	- name: Verify installation
	env:
	PYTHONPATH: ${{ github.workspace }}
	run: \|
	export PYTHONPATH=${{ github.workspace }}:$PYTHONPATH
	python -c "import sys; print('Python version:', sys.version)"
	python -c "import sys; print('Python path:', sys.path)"
	python -c "import app; print('✓ App imported successfully')" \|\| (echo "✗ App import failed" && exit 1)
	python -c "from app.utils.config import GEMINI_API_KEY; print('✓ Config imported')" \|\| echo "⚠ Config import warning"

	- name: Run tests
	env:
	# Set dummy API keys for testing (tests should handle missing keys gracefully)
	GEMINI_API_KEY: "test_key_1234567890abcdef"
	NCBI_API_KEY: "test_ncbi_key_1234567890"
	EMAIL: "test@example.com"
	PYTHONPATH: ${{ github.workspace }}
	run: \|
	export PYTHONPATH=${{ github.workspace }}:$PYTHONPATH
	pytest tests/ -v --tb=short --maxfail=10 --cov=app --cov-report=xml --cov-report=term-missing --cov-fail-under=50

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	file: ./coverage.xml
	flags: unittests
	name: codecov-umbrella
	fail_ci_if_error: false

	lint:
	name: Lint Code
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Lint with Black and flake8 using Docker
	run: \|
	docker run --rm \
	-v ${{ github.workspace }}:/workspace \
	-w /workspace \
	python:3.11-slim \
	bash -c "
	apt-get update -qq && apt-get install -y -qq gcc > /dev/null 2>&1 && \
	pip install --quiet --no-cache-dir black>=23.0.0 flake8>=6.0.0 && \
	echo '=== Running Black (check mode) ===' && \
	black --check --diff app/ tests/ cli.py main.py && \
	echo '=== Running flake8 ===' && \
	flake8 app/ tests/ cli.py main.py --max-line-length=120 --extend-ignore=E203,W503,E501 --exclude=__pycache__,*.pyc
	"

	type-check:
	name: Type Check
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PYTHON_DEFAULT_VERSION }}
	cache: 'pip'

	- name: Install type checking dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install mypy>=1.5.0 types-requests types-PyYAML

	- name: Run mypy
	run: \|
	mypy app/ --config-file mypy.ini \|\| (echo "⚠️ Type checking found issues. Review and fix type errors." && exit 1)
	continue-on-error: false # Type checking is now required

	security:
	name: Security Scan
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PYTHON_DEFAULT_VERSION }}
	cache: 'pip'

	- name: Install security scanning tools
	run: \|
	python -m pip install --upgrade pip
	pip install bandit safety

	- name: Run Bandit security scan
	run: \|
	bandit -r app/ -f json -o bandit-report.json
	bandit -r app/ -ll
	continue-on-error: false # Security issues must be addressed

	- name: Check dependencies with Safety
	run: \|
	pip install -e ".[dev]"
	safety check --json
	safety check
	continue-on-error: false # Vulnerable dependencies must be fixed

	docker-build:
	name: Docker Build Test
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3

	- name: Build Docker image
	uses: docker/build-push-action@v5
	with:
	context: .
	file: ./Dockerfile
	push: false
	load: true
	tags: bioanalyzer-backend:test
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- name: Test Docker image
	run: \|
	docker run --rm bioanalyzer-backend:test python -c "import app; print('Docker image works!')"

	all-checks:
	name: All Checks Summary
	runs-on: ubuntu-latest
	needs: [test, lint, type-check, security, docker-build]
	if: always()

	steps:
	- name: Check job status
	run: \|
	echo "## CI/CD Pipeline Status" >> $GITHUB_STEP_SUMMARY
	echo "" >> $GITHUB_STEP_SUMMARY
	echo "\| Job \| Status \|" >> $GITHUB_STEP_SUMMARY
	echo "\|-----\|--------\|" >> $GITHUB_STEP_SUMMARY
	echo "\| Tests \| ${{ needs.test.result }} \|" >> $GITHUB_STEP_SUMMARY
	echo "\| Lint \| ${{ needs.lint.result }} \|" >> $GITHUB_STEP_SUMMARY
	echo "\| Type Check \| ${{ needs.type-check.result }} \|" >> $GITHUB_STEP_SUMMARY
	echo "\| Security \| ${{ needs.security.result }} \|" >> $GITHUB_STEP_SUMMARY
	echo "\| Docker Build \| ${{ needs.docker-build.result }} \|" >> $GITHUB_STEP_SUMMARY
	echo "" >> $GITHUB_STEP_SUMMARY

	# Fail if any critical check failed
	if [ "${{ needs.test.result }}" != "success" ] \|\| \
	[ "${{ needs.lint.result }}" != "success" ] \|\| \
	[ "${{ needs.type-check.result }}" != "success" ] \|\| \
	[ "${{ needs.security.result }}" != "success" ] \|\| \
	[ "${{ needs.docker-build.result }}" != "success" ]; then
	echo "❌ One or more critical checks failed!" >> $GITHUB_STEP_SUMMARY
	echo "Test: ${{ needs.test.result }}" >> $GITHUB_STEP_SUMMARY
	echo "Lint: ${{ needs.lint.result }}" >> $GITHUB_STEP_SUMMARY
	echo "Type-check: ${{ needs.type-check.result }}" >> $GITHUB_STEP_SUMMARY
	echo "Security: ${{ needs.security.result }}" >> $GITHUB_STEP_SUMMARY
	echo "Docker-build: ${{ needs.docker-build.result }}" >> $GITHUB_STEP_SUMMARY
	exit 1
	else
	echo "✅ All checks passed!" >> $GITHUB_STEP_SUMMARY
	fi

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Add CODEOWNERS file for code review requirements #10

Workflow file

Add CODEOWNERS file for code review requirements #10

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Workflow file for this run

GitHub Actions / .github/workflows/ci.yml