Makefile

.PHONY: help install install-dev test test-unit test-integration test-cov lint format type-check clean build docs

help:
	@echo "Identifiability Diagnostic Framework - Development Commands"
	@echo ""
	@echo "Installation:"
	@echo "  make install              Install package"
	@echo "  make install-dev          Install with dev dependencies"
	@echo ""
	@echo "Testing:"
	@echo "  make test                 Run all tests"
	@echo "  make test-unit            Run unit tests only"
	@echo "  make test-integration     Run integration tests only"
	@echo "  make test-cov             Run tests with coverage report"
	@echo ""
	@echo "Code Quality:"
	@echo "  make lint                 Run all linters (flake8, mypy, pylint)"
	@echo "  make format               Format code (black, isort)"
	@echo "  make type-check           Type checking with mypy"
	@echo ""
	@echo "Building:"
	@echo "  make build                Build distribution packages"
	@echo "  make clean                Clean build artifacts"
	@echo ""
	@echo "Examples:"
	@echo "  make examples             Run example scripts"

install:
	pip install -e .

install-dev:
	pip install -e ".[dev]"

test:
	pytest tests/ -v --tb=short

test-unit:
	pytest tests/unit -v --tb=short

test-integration:
	pytest tests/integration -v --tb=short

test-cov:
	pytest tests/ -v --cov=src/identifiability_diagnostic --cov-report=html --cov-report=term-missing
	@echo "Coverage report generated in htmlcov/index.html"

lint: lint-flake8 lint-mypy lint-pylint
	@echo "✓ All linters passed"

lint-flake8:
	flake8 src/identifiability_diagnostic tests --max-line-length=100

lint-mypy:
	mypy src/identifiability_diagnostic --ignore-missing-imports || true

lint-pylint:
	pylint src/identifiability_diagnostic --exit-zero || true

format:
	black src/identifiability_diagnostic tests examples
	isort src/identifiability_diagnostic tests examples
	@echo "✓ Code formatted"

type-check:
	mypy src/identifiability_diagnostic --ignore-missing-imports

build: clean
	python -m build
	@echo "✓ Build complete - dist/ directory ready"

clean:
	rm -rf build/ dist/ *.egg-info
	find . -type d -name __pycache__ -exec rm -rf {} +
	find . -type f -name "*.pyc" -delete
	rm -rf .pytest_cache .mypy_cache .coverage htmlcov
	@echo "✓ Cleanup complete"

examples:
	python examples/basic_usage.py

run-main:
	python main.py --config config/parameters.yaml --verbose

run-main-test:
	python main.py --config config/parameters.yaml --test

all: clean install-dev lint test-cov
	@echo "✓ Full test suite passed"