Makefile

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# GLOBALS                                                                       #
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PYTHON=python3
R=Rscript

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# COMMANDS                                                                      #
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all: venv requirements all_from_make
.PHONY: all

# Environment

venv:
	$(PYTHON) -m venv venv
	mkdir -p venv/lib/R/site-library
	echo 'R_LIBS_SITE="$$VIRTUAL_ENV/lib/R/site-library"' >> venv/bin/activate
	echo 'export R_LIBS_SITE' >> venv/bin/activate

ACTIVATE_ENV=. venv/bin/activate

requirements: venv
	$(ACTIVATE_ENV); \
	pip install -r requirements.txt; \
	${R} requirements.R
.PHONY: requirements

update-requirements: venv
	$(ACTIVATE_ENV); pip install -Ur requirements.txt
.PHONY: update-requirements

# Tools

clean:
	find src/ -name "*.pyc" -exec rm {} \;
	find src/ -name "__pycache__" -exec rmdir {} \;
	find notebooks/ -name "*.html" -exec rm {} \;
	find reports/ -name "*.md" -exec rm {} \;
	find reports/ -name "*.html" ! -name pandoc-template.html -exec rm {} \;
	-rm -f reports/figures/*

.PHONY: clean

lint:
	$(ACTIVATE_ENV); flake8 --exclude=docs/conf.py,venv .
.PHONY: lint

# Help

help:
	@echo "Available make commands:"
	@echo "help                Show this help"
	@echo "clean               Delete all compiled Python files"
	@echo "venv                Make virtual environment"
	@echo "requirements        Install Python dependencies"
	@echo "update-requirements Update Python dependencies to their latest version"
	@echo "all                 Make all data, models and reports"


# Load environment and make files with project rules.

Makefile: ;
%: requirements
	$(ACTIVATE_ENV); snakemake $@