Makefile

.PHONY: test

export PYTHONPATH:=$PYTHONPATH:$(shell pwd)
export PYSPARK_PYTHON:=$(shell which python)
export PYSPARK_DRIVER_PYTHON:=$(shell which python)

test: unit-test integration-test

test-ut-one-step:
	cd tests/unit_tests && pytest -vv -s -k $(test)

test-it-one-step:
	cd tests/integration_tests && pytest -vv -s -k $(test)

test-it-one-step-profile: clear-hard-filter-checkpoints
	cd tests/integration_tests && \
	python -m cProfile -o profile.stats -m pytest -vv -s -k $(test) && \
	snakeviz --hostname 0.0.0.0 $(shell pwd)/tests/integration_tests/profile.stats

integration-test-trios: clear-ht clear-logs
	cd tests/integration_tests && pytest -k test_trios_

integration-test-non-trios: clear-ht clear-logs
	cd tests/integration_tests && pytest -k test_non_trios_


integration-test-coverage: clear-ht clear-logs
	cd tests/integration_tests && pytest -k test_trios_ --cov=../..


unit-test:
	cd tests/unit_tests && pytest

unit-test-coverage:
	cd tests/unit_tests && pytest --cov=../..

clear-hard-filter-checkpoints:
	rm -rf tests/integration_tests/integration-data/annotations/testhash/json_dump/* || true

clear-logs:
	rm hail*.log || true
	rm hlrun_* || true
	rm tests/unit_tests/hail*.log || true
	rm tests/integration_tests/hail*.log || true

clear-ht:
	rm -rf tests/integration_tests/matrixtables/* || true


sync-to-private:
	git remote add origin-private git@github.com:wtsi-hgi/wes-qc-analysis.git || true
	git switch main
	git pull
	git push origin-private

update:
	git fetch origin main:main
	git rebase main