Makefile

SHELL:=/bin/bash

PYTHON_VERSION=3.9.19
PYTHON_SYS=python3.9
VIRTUAL_ENV=env
PYTHON_ENV=${VIRTUAL_ENV}/bin/python3
JAVA_VERSION=21
ARCHITECTURE=amd64
BUILD_REF_STAGE=build-ref
ENGINE=docker

ifeq ($(ENGINE),podman)
	PODMAN_PARAM=--format docker
	export USE_PODMAN=true
endif

# .ONESHELL:
DEFAULT_GOAL: install
.PHONY: help clean build build-ref integration-tests unit-tests mypy check format \
		install-nextflow install-python install-docker install-java install-podman

# Colors for echos 
ccend = $(shell tput sgr0)
ccbold = $(shell tput bold)
ccgreen = $(shell tput setaf 2)
ccso = $(shell tput smso)

mypy: venv ## >> run mypy type checker
	@echo ""
	@echo "$(ccso)--> Running mypy $(ccend)"
	$(PYTHON_ENV) -m mypy bin/calib_dedup/
	$(PYTHON_ENV) -m mypy bin/fastp/
	$(PYTHON_ENV) -m mypy bin/vidjil/
	$(PYTHON_ENV) -m mypy bin/igblast/
	$(PYTHON_ENV) -m mypy bin/cdr3nt_error_corrector/

check: venv ## >> run ruff linter
	@echo ""
	@echo "$(ccso)--> Running ruff check $(ccend)"
	$(PYTHON_ENV) -m ruff check bin/calib_dedup/ bin/fastp/ bin/vidjil/ bin/igblast/ bin/cdr3nt_error_corrector/

format: venv ## >> run ruff formatter
	@echo ""
	@echo "$(ccso)--> Running ruff format $(ccend)"
	$(PYTHON_ENV) -m ruff format bin/calib_dedup/ bin/fastp/ bin/vidjil/ bin/igblast/ bin/cdr3nt_error_corrector/

integration-tests: venv ## >> run tests for all workflows via pytest and pytest-workflow tool
	@echo ""
	@echo "$(ccso)--> Running workflow tests $(ccend)"
	$(PYTHON_ENV) -m pytest tests -vv --kwdof --tag integration-tests

unit-tests: venv ## >> run tests for all steps via pytest tool
	@echo ""
	@echo "$(ccso)--> Running steps tests $(ccend)"
	$(PYTHON_ENV) -m pytest bin/pyumi/unit_tests -vv
#	$(PYTHON_ENV) -m pytest bin/calib_dedup/unit_tests -vv
	$(PYTHON_ENV) -m pytest tests -vv --kwdof --tag unit-tests
	$(PYTHON_ENV) -m pytest bin/cdr3nt_error_corrector/unit_tests -vv

tests: venv ##@main >> run integration and unit tests
	@echo ""
	@echo "$(ccso)--> Running integration and unit tests $(ccend)"
	$(MAKE) unit-tests
	$(MAKE) integration-tests

clean: ## >> remove docker images, python environment and nextflow build files
	@echo ""
	@echo "$(ccso)--> Removing temporary files and images $(ccend)"
	$(ENGINE) rmi -f downloader-image \
		pyumi-tool pyumi-image \
		calib_dedup-tool calib_dedup-image \
		fastp-tool fastp-image \
		vidjil-tool vidjil-image \
		igblast-tool igblast-image \
		cdr3nt_error_corrector-tool cdr3nt_error_corrector-image
	rm -rf $(VIRTUAL_ENV) \
		.nextflow.log* work .nextflow nextflow

build-ref-image:
	@echo ""
	@echo "$(ccso)--> Build images of reference generators $(ccend)"
	$(ENGINE) build --target build-ref -t $(STEP)-$(BUILD_REF_STAGE) $(PODMAN_PARAM) bin/$(STEP)/

build-igblast-ref-major: ## >> build an archive with igblast vdj reference with only major allele (*01)
	@echo ""
	@echo "$(ccso)--> Build a vdj reference with all alleles (*01) for igblast $(ccend)"
	$(ENGINE) run --rm -v $(pwd)/bin/igblast:/work igblast-$(BUILD_REF_STAGE) -o /work/igblast.reference.major_allele.tar.gz

build-igblast-ref-all: ## >> build an archive with igblast vdj reference with all alleles
	@echo ""
	@echo "$(ccso)--> Build a vdj reference with all alleles (*01, *02, etc.) for igblast $(ccend)"
	$(ENGINE) run --rm -v $(pwd)/bin/igblast:/work igblast-$(BUILD_REF_STAGE) -a -o /work/igblast.reference.all_alleles.tar.gz

build-vidjil-ref: ## >> build an archive with vidjil reference
	@echo ""
	@echo "$(ccso)--> Build a vdj reference for vidjil $(ccend)"
	bash bin/vidjil/build_ref.sh
	mv /tmp/vidjil.germline.tar.gz bin/vidjil/

build-olga-models: ## >> build an archive with olga models
	@echo ""
	@echo "$(ccso)--> Build olga models for cdr3nt-error-corrector $(ccend)"
	bash bin/cdr3nt_error_corrector/build_ref.sh
	mv /tmp/olga-models.tar.gz bin/cdr3nt_error_corrector/

build-ref: ##@main >> build all references
	@echo ""
	@echo "$(ccso)--> Build all references $(ccend)"
	$(MAKE) build-ref-image STEP=igblast
	$(MAKE) build-igblast-ref-major
	$(MAKE) build-igblast-ref-all
	$(MAKE) build-vidjil-ref
	$(MAKE) build-olga-models

build: ##@main >> build docker images, the virtual environment and install requirements
	@echo ""
	@echo "$(ccso)--> Build $(ccend)"
	$(MAKE) clean
	$(MAKE) install-nextflow
	$(MAKE) build-step-image STEP=downloader STAGE=image
	for step in pyumi calib_dedup fastp vidjil igblast cdr3nt_error_corrector ; do \
    	$(MAKE) build-step-image STEP=$$step STAGE=image ; \
    	$(MAKE) build-step-image STEP=$$step STAGE=tool ; \
	done
	$(MAKE) update
	nf-core schema build --no-prompts
	chmod +x pyigmap

venv: $(VIRTUAL_ENV)

$(VIRTUAL_ENV): ## >> setup the virtual environment
	@echo "$(ccso)--> Install and setup virtualenv $(ccend)"
	$(PYTHON_SYS) -m pip install --upgrade pip
	$(PYTHON_SYS) -m pip install virtualenv
	virtualenv $(VIRTUAL_ENV)

update: venv ## >> update requirements.txt inside the virtual environment
	@echo "$(ccso)--> Updating packages $(ccend)"
	$(PYTHON_ENV) -m pip install -r bin/pyumi/requirements.txt
	$(PYTHON_ENV) -m pip install -r bin/cdr3nt_error_corrector/requirements.txt
	$(PYTHON_ENV) -m pip install pytest==8.1.1 pytest-workflow==2.1.0 ruff==0.4.2 mypy==1.10.0 nf-core==2.14.1

install-python: ## >> install a python
	curl -fL http://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tgz > /tmp/python.tgz
	mkdir -p /tmp/python
	tar xzvf /tmp/python.tgz --one-top-level=/tmp/python --strip-component 1
	cd /tmp/python && \
		./configure --enable-optimizations && \
		make -j 8 && sudo make altinstall
	sudo apt install ${PYTHON_SYS}-distutils
	sudo rm -rf /tmp/python.tgz /tmp/python

install-docker: ## >> install a docker
	curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
	sudo add-apt-repository "deb [arch=${ARCHITECTURE}] https://download.docker.com/linux/ubuntu $(shell lsb_release -cs) stable"
	sudo apt-get update
	sudo apt-get -y -o Dpkg::Options::="--force-confnew" install docker-ce

install-podman: ## >> install a Podman
	sudo apt-get update
	sudo apt-get -y install podman

install-java: ## >> install a java
	curl -fL https://download.oracle.com/java/${JAVA_VERSION}/latest/jdk-${JAVA_VERSION}_linux-x64_bin.tar.gz > /tmp/java.tar.gz
	mkdir -p /tmp/java-${JAVA_VERSION}
	tar xzvf /tmp/java.tar.gz --one-top-level=/tmp/java-${JAVA_VERSION} --strip-component 1
	sudo mv /tmp/java-${JAVA_VERSION} /usr/local/bin/
	@echo "export JAVA_HOME=/usr/local/bin/java-${JAVA_VERSION}" >> ~/.bashrc
	@echo 'export PATH=$$JAVA_HOME/bin:$$PATH' >> ~/.bashrc
	export JAVA_HOME=/usr/local/bin/java-${JAVA_VERSION}
	export PATH=$$JAVA_HOME/bin:$$PATH
	@java -version
	rm /tmp/java.tar.gz

install-nextflow: ## >> install a NextFlow
	@java --version
	curl -s https://get.nextflow.io | bash

install-gh:
	curl -sS https://webi.sh/gh | sh

install-cliff: ## >> Install git-cliff tool
	@echo ""
	@echo "$(ccso)--> Installing git-cliff tool $(ccend)"
	curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
	$$HOME/.cargo/bin/cargo install --version 2.6.1 git-cliff

changelog: install-cliff ## >> Update CHANGELOG.md
	@echo ""
	@echo "$(ccso)--> Updating CHANGELOG.md $(ccend)"
	git-cliff --tag $(TAG) --bump -o CHANGELOG.md
	git add CHANGELOG.md && git commit -m "chore(release): prepare for $(TAG)"
	git show

release: install-gh changelog
	git tag $(TAG) && git push origin $(TAG)
	git push
	git cliff --strip all --latest | gh release create $(TAG) --notes-file -

build-step-image:
	@$(ENGINE) version
	$(ENGINE) build --target $(STAGE) -t $(STEP)-$(STAGE) $(PODMAN_PARAM) bin/$(STEP)

install: ## Install and check dependencies
	$(MAKE) install-nextflow
	$(MAKE) build-ref
	$(MAKE) build-step-image STEP=downloader STAGE=image
	for step in pyumi calib_dedup fastp vidjil igblast cdr3nt_error_corrector ; do \
    	$(MAKE) build-step-image STEP=$$step STAGE=image ; \
	done
	chmod +x pyigmap

# And add help text after each target name starting with '\#\#'
# A category can be added with @category
HELP_FUN = \
	%help; \
	while(<>) { push @{$$help{$$2 // 'options'}}, [$$1, $$3] if /^([a-zA-Z\-\$\(]+)\s*:.*\#\#(?:@([a-zA-Z\-\)]+))?\s(.*)$$/ }; \
	print "usage: make [target]\n\n"; \
	for (sort keys %help) { \
	print "${WHITE}$$_:${RESET}\n"; \
	for (@{$$help{$$_}}) { \
	$$sep = " " x (32 - length $$_->[0]); \
	print "  ${YELLOW}$$_->[0]${RESET}$$sep${GREEN}$$_->[1]${RESET}\n"; \
	}; \
	print "\n"; }

help: ##@other >> Show this help.
	@perl -e '$(HELP_FUN)' $(MAKEFILE_LIST)
	@echo ""
	@echo "Note: to activate the environment in your local shell type:"
	@echo "   $$ source $(VIRTUAL_ENV)/bin/activate"