Makefile

include common_parameters.env
export

$(if $(wildcard ../sgpy),,$(error Why aren't you in the sgpy directory?))

SHELL = /bin/sh
CURRENT_UID := $(shell id -u)
CURRENT_GID := $(shell id -g)
export CURRENT_UID
export CURRENT_GID


## help	:	Print help info
help : Makefile
	@sed -n 's/^##//p' $<

## clean	:	Clean temporary files, INCLUDES DELETING THE NEXTFLOW TEMPORY WORK DIRECTORY
clean:
	@echo "Cleaning up temporary Python files..."
	find . -type f -name "*.py[co]" -exec rm -r {} +
	find . -type d -name "__pycache__" -exec rm -r {} +
	find . -type d -name "htmlcov" -exec rm -r {} +
	find . -type d -name "dist" -exec rm -r {} +
	find . -type d -name "build" -exec rm -r {} +
	find . -type d -name ".eggs" -exec rm -r {} +
	find . -type d -name "*.egg-info" -exec rm -r {} +
	find . -type d -name ".pytest_cache" -exec rm -r {} +
	find . -type d -name ".tox" -exec rm -r {} +
	find . -name ".coverage" -exec rm -r {} +
	find . -name "coverage.xml" -exec rm -r {} +
	find . -name ".nextflow.log.*" -exec rm -r {} +
	find . -type d -name ".nextflow" -exec rm -r {} +
	find . -name ".nextflow.log" -exec rm {} +
	find . -type d -name "work" -exec rm -r {} +
	find . -type d -name ".pytest_cache" -exec rm -r {} +
	find . -type d -name "__pycache__" -exec rm -r {} +
	find . -type d -name "site" -exec rm -r {} +
	find . -type d -name ".tox" -exec rm -r {} +


## create_mamba :	Create a conda enviornment with socialgene
create_mamba:
	mamba env create --file environment.yml


## socialgene_image	:	Make socialgene python docker image
build_docker_image: clean
	docker build -f Dockerfile --tag socialgene:latest .

build_docker_image2: clean
	docker build -f Dockerfileantismash --tag antismashsg:latest .

## install :	Install the socialgene python package
install:
	pip install -e .[ci]

## pytest	:	Run Python pacakge unit tests
pytest: clean install
	pytest tests/python -v --ignore=socialgene/entrypoints/export_protein_loci_assembly_tables.py 	 --cov=./socialgene --cov-report=xml:./coverage.xml --cov-report html tests/python
	xdg-open htmlcov/index.html

## pytestnf :	Run Nextflow pytest tests (first runs clean, install python and  nextflow test run)
pytestnf: clean install testnf
	coverage run --source=./socialgene --module pytest ./socialgene/tests/nextflow --neo4j_outdir $(neo4j_outdir)

run_ci: clean install pytest
	@echo "TESTING WITH FLAKE8"
	flake8 . --ignore E203,E501,W503 --count --show-source
	@echo "TESTING WITH BLACK"
	black --check . --target-version py310
	@echo "Checking package imports with isort"
	isort . --settings-path pyproject.toml --check-only

## run_ci :	Uploda to PyPi
run_cd: run_ci clean
	python3 -m pip install .[cd]
	python3 -m build ./socialgene
	python3 -m twine upload --repository testpypi ./socialgene/dist/*

# https://stackoverflow.com/a/6273809/1826109
%:
	@:
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